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output/comprehensive_fixes/results/all_comprehensive_fixes.json

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+{
+  "fix_b_utr": {
+    "pancreas": {
+      "dataset": "pancreas",
+      "n_targets": 176,
+      "n_matched": 166,
+      "utr_length_destab_median": 2420.0,
+      "utr_length_stab_median": 2432.0,
+      "utr_length_mw_p": 0.6757002839765559,
+      "au_content_destab_median": 0.576214405360134,
+      "au_content_stab_median": 0.5984087102177554,
+      "au_content_mw_p": 0.9793488740930798,
+      "spearman_r_vs_utr_length": -0.136319961802761,
+      "spearman_p_vs_utr_length": 0.07989891535893835,
+      "spearman_r_vs_au_content": -0.15385614313541593,
+      "spearman_p_vs_au_content": 0.04780261384186119
+    },
+    "dentate_gyrus": {
+      "dataset": "dentate_gyrus",
+      "n_targets": 124,
+      "n_matched": 118,
+      "utr_length_destab_median": 2522.5,
+      "utr_length_stab_median": 1965.0,
+      "utr_length_mw_p": 0.02493904657469992,
+      "au_content_destab_median": 0.5893077940041419,
+      "au_content_stab_median": 0.5942052381868609,
+      "au_content_mw_p": 0.4760398682988743,
+      "spearman_r_vs_utr_length": 0.12453139579705842,
+      "spearman_p_vs_utr_length": 0.1790799103865216,
+      "spearman_r_vs_au_content": -0.04015426248726348,
+      "spearman_p_vs_au_content": 0.6659465074321518
+    },
+    "neuroblastoma": {
+      "dataset": "neuroblastoma",
+      "n_targets": 85,
+      "n_matched": 81,
+      "utr_length_destab_median": 4230.5,
+      "utr_length_stab_median": 3594.0,
+      "utr_length_mw_p": 0.1277627029361753,
+      "au_content_destab_median": 0.6261289733287869,
+      "au_content_stab_median": 0.6113207547169811,
+      "au_content_mw_p": 0.2840004975109969,
+      "spearman_r_vs_utr_length": 0.07378048780487804,
+      "spearman_p_vs_utr_length": 0.51272750323782,
+      "spearman_r_vs_au_content": 0.12138663053297198,
+      "spearman_p_vs_au_content": 0.280366151780597
+    }
+  },
+  "fix_d_hub_consistency": {
+    "pairwise_correlations": [
+      {
+        "dataset_a": "dentate_gyrus",
+        "dataset_b": "neuroblastoma",
+        "spearman_r": 0.6207522318391883,
+        "spearman_p": 0.07443796489097941,
+        "n_shared": 9
+      },
+      {
+        "dataset_a": "dentate_gyrus",
+        "dataset_b": "pancreas",
+        "spearman_r": 0.34788117561515225,
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+        "n_shared": 17
+      },
+      {
+        "dataset_a": "neuroblastoma",
+        "dataset_b": "pancreas",
+        "spearman_r": 0.6906864796671202,
+        "spearman_p": 0.012888876660556747,
+        "n_shared": 12
+      }
+    ],
+    "universal_hubs": [
+      {
+        "rbp": "YBX1",
+        "n_datasets_top20": 3,
+        "datasets": "dentate_gyrus, neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 550,
+        "targets_neuroblastoma": 21,
+        "targets_pancreas": 158
+      },
+      {
+        "rbp": "FUS",
+        "n_datasets_top20": 2,
+        "datasets": "neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 0,
+        "targets_neuroblastoma": 14,
+        "targets_pancreas": 32
+      },
+      {
+        "rbp": "HNRNPA1",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 209,
+        "targets_neuroblastoma": 0,
+        "targets_pancreas": 166
+      },
+      {
+        "rbp": "HNRNPA2B1",
+        "n_datasets_top20": 2,
+        "datasets": "neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 0,
+        "targets_neuroblastoma": 46,
+        "targets_pancreas": 12
+      },
+      {
+        "rbp": "ELAVL1",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 129,
+        "targets_neuroblastoma": 0,
+        "targets_pancreas": 43
+      },
+      {
+        "rbp": "HNRNPC",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 109,
+        "targets_neuroblastoma": 3,
+        "targets_pancreas": 29
+      },
+      {
+        "rbp": "RBFOX3",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 197,
+        "targets_neuroblastoma": 0,
+        "targets_pancreas": 70
+      },
+      {
+        "rbp": "SRSF3",
+        "n_datasets_top20": 2,
+        "datasets": "neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 0,
+        "targets_neuroblastoma": 11,
+        "targets_pancreas": 144
+      },
+      {
+        "rbp": "TRA2B",
+        "n_datasets_top20": 2,
+        "datasets": "neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 0,
+        "targets_neuroblastoma": 6,
+        "targets_pancreas": 47
+      },
+      {
+        "rbp": "MATR3",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 134,
+        "targets_neuroblastoma": 0,
+        "targets_pancreas": 27
+      },
+      {
+        "rbp": "PTBP1",
+        "n_datasets_top20": 2,
+        "datasets": "neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 0,
+        "targets_neuroblastoma": 6,
+        "targets_pancreas": 27
+      },
+      {
+        "rbp": "HNRNPD",
+        "n_datasets_top20": 2,
+        "datasets": "neuroblastoma, pancreas",
+        "targets_dentate_gyrus": 0,
+        "targets_neuroblastoma": 18,
+        "targets_pancreas": 48
+      },
+      {
+        "rbp": "ELAVL4",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 73,
+        "targets_neuroblastoma": 0,
+        "targets_pancreas": 24
+      },
+      {
+        "rbp": "STAU2",
+        "n_datasets_top20": 2,
+        "datasets": "dentate_gyrus, pancreas",
+        "targets_dentate_gyrus": 44,
+        "targets_neuroblastoma": 0,
+        "targets_pancreas": 15
+      }
+    ],
+    "dataset_hubs": {
+      "dentate_gyrus": {
+        "YBX1": 550,
+        "RBFOX1": 230,
+        "CELF2": 214,
+        "HNRNPA1": 209,
+        "RBFOX3": 197,
+        "ELAVL3": 194,
+        "RBFOX2": 143,
+        "MATR3": 134,
+        "ELAVL1": 129,
+        "MBNL2": 118
+      },
+      "neuroblastoma": {
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+        "PABPC1": 28,
+        "YBX1": 21,
+        "HNRNPD": 18,
+        "HNRNPU": 18,
+        "PRPF8": 17,
+        "SNRNP200": 16,
+        "FUS": 14,
+        "HNRNPK": 14,
+        "NCL": 12
+      },
+      "pancreas": {
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+        "YBX1": 158,
+        "SRSF3": 144,
+        "RBFOX3": 70,
+        "HNRNPD": 48,
+        "TRA2B": 47,
+        "ELAVL1": 43,
+        "FUS": 32,
+        "SRSF1": 30,
+        "ZFP36L1": 30
+      }
+    },
+    "n_universal": 14,
+    "n_tissue_specific": 31
+  },
+  "fix_c_nb_depmap": {
+    "neuroblastoma": {
+      "n_hub_rbps": 20,
+      "n_hub_matched": 20,
+      "n_nonhub_matched": 28,
+      "nb_hub_mean_dep": -1.1231941630752047,
+      "nb_nonhub_mean_dep": -0.6345991668039,
+      "nb_mw_p": 0.024066198109790972,
+      "all_hub_mean_dep": -1.1200964888610585,
+      "all_nonhub_mean_dep": -0.6168147386880988,
+      "all_mw_p": 0.02072830347215501,
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+      "hub_nb_mean": -1.1231941630752047,
+      "hub_non_nb_mean": -1.1199911625364276,
+      "ntargets_dep_spearman_r": -0.2594713478934196,
+      "ntargets_dep_spearman_p": 0.07492474053632316
+    },
+    "pancreas": {
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+      "n_hub_matched": 20,
+      "n_nonhub_matched": 137,
+      "nb_hub_mean_dep": -0.9730124214105149,
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+      "nb_mw_p": 0.006820384207358076,
+      "all_hub_mean_dep": -0.9997965508106808,
+      "all_nonhub_mean_dep": -0.4898479613026557,
+      "all_mw_p": 0.004014393322680695,
+      "nb_specificity_p": 0.5697845131323614,
+      "hub_nb_mean": -0.9730124214105149,
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+      "ntargets_dep_spearman_r": -0.09211910713859293,
+      "ntargets_dep_spearman_p": 0.2511886468436864
+    },
+    "dentate_gyrus": {
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+      "n_nonhub_matched": 27,
+      "nb_hub_mean_dep": -0.7164812943730803,
+      "nb_nonhub_mean_dep": -0.3771843463296336,
+      "nb_mw_p": 0.0893471950344088,
+      "all_hub_mean_dep": -0.6933051686072866,
+      "all_nonhub_mean_dep": -0.3742576462007085,
+      "all_mw_p": 0.13860968767464932,
+      "nb_specificity_p": 0.5377136358338882,
+      "hub_nb_mean": -0.7164812943730803,
+      "hub_non_nb_mean": -0.6923244154397531,
+      "ntargets_dep_spearman_r": -0.2586847838682696,
+      "ntargets_dep_spearman_p": 0.07913620588500175
+    }
+  },
+  "fix_a_per_cell": {
+    "n_cells_total": 7404,
+    "n_cells_valid": 7403,
+    "mean_gamma_corr": 0.6400740651477818,
+    "mean_raw_corr": 0.6372983859554561,
+    "median_gamma_corr": 0.6462974763496186,
+    "median_raw_corr": 0.6410144251697661,
+    "wilcoxon_p": 1.0308648272252094e-297,
+    "gamma_better_frac": 0.7224098338511414,
+    "raw_better_frac": 0.27759016614885856,
+    "mean_gamma_cv": 3.524893548703429,
+    "mean_raw_cv": 1.2779634798135078,
+    "cv_wilcoxon_p": 1.0
+  },
+  "fix_e_coherence": {
+    "n_clusters_tested": 19,
+    "summary_by_method": {
+      "scPTR_gamma": {
+        "n_clusters": 19,
+        "mean_invisibility": 0.08081366305582617,
+        "total_sig_pathways": 2622,
+        "total_expected_pathways": 180,
+        "mean_diff_genes": 3719.157894736842
+      },
+      "raw_u_s_ratio": {
+        "n_clusters": 19,
+        "mean_invisibility": 0.15686803808631866,
+        "total_sig_pathways": 2372,
+        "total_expected_pathways": 168,
+        "mean_diff_genes": 3388.4736842105262
+      },
+      "unspliced_only": {
+        "n_clusters": 18,
+        "mean_invisibility": 0.25947572973867256,
+        "total_sig_pathways": 2258,
+        "total_expected_pathways": 192,
+        "mean_diff_genes": 5208.888888888889
+      }
+    }
+  }
+}

output/comprehensive_fixes/results/coherence_ablation.csv

@@ -0,0 +1,57 @@
+dataset,cluster,method,n_cells,n_subclusters,sil_method,sil_expr,invisibility,n_diff_genes,n_sig_pathways,n_expected_pathways,mean_utr_length_sig,mean_utr_length_bg,utr_enrichment_p
+pancreas,Alpha,scPTR_gamma,481,2,0.15257389843463898,0.1845233291387558,-0.03194943070411682,6591,194,14,1998.6814802577235,1950.8020612598727,0.04482401420332316
+pancreas,Alpha,raw_u_s_ratio,481,2,0.24246463179588318,0.16570322215557098,0.0767614096403122,5798,144,14,1963.9166666666667,1950.8020612598727,0.329069471769189
+pancreas,Alpha,unspliced_only,481,2,0.519585907459259,0.23214322328567505,0.287442684173584,8289,152,12,1998.8037138927098,1950.8020612598727,0.02821633147086173
+pancreas,Beta,scPTR_gamma,591,2,0.15817323327064514,0.20982347428798676,-0.051650241017341614,6807,194,12,1983.556834532374,1950.8020612598727,0.13478810552039933
+pancreas,Beta,raw_u_s_ratio,591,2,0.25216004252433777,-0.03533986583352089,0.28749990835785866,4401,76,6,1990.2747770069375,1950.8020612598727,0.09754411335221075
+pancreas,Beta,unspliced_only,591,2,0.7582722306251526,0.26660215854644775,0.49167007207870483,8966,148,16,2017.6105543574781,1950.8020612598727,0.005409153010339139
+pancreas,Delta,scPTR_gamma,70,2,0.27850592136383057,0.13610050082206726,0.1424054205417633,5226,114,6,1999.2952006619776,1950.8020612598727,0.04757171493385224
+pancreas,Delta,raw_u_s_ratio,70,2,0.32580822706222534,0.1512812227010727,0.17452700436115265,5222,112,6,2003.0093264248706,1950.8020612598727,0.037547029721860845
+pancreas,Delta,unspliced_only,70,2,0.48396214842796326,0.13379165530204773,0.3501704931259155,6483,98,6,2050.1647855530473,1950.8020612598727,1.571097517731684e-05
+pancreas,Ductal,scPTR_gamma,916,2,0.19152724742889404,0.30967360734939575,-0.11814635992050171,7226,200,14,1951.9572119745994,1950.8020612598727,0.2975459457127886
+pancreas,Ductal,raw_u_s_ratio,916,2,0.24733364582061768,0.3008851706981659,-0.05355152487754822,7025,166,8,1949.9856898428993,1950.8020612598727,0.32099788504212234
+pancreas,Ductal,unspliced_only,916,2,0.5851033926010132,0.14889667928218842,0.43620671331882477,8275,154,10,1980.8519835841314,1950.8020612598727,0.11678605803378844
+pancreas,Epsilon,scPTR_gamma,142,3,0.19351229071617126,-0.05613316595554352,0.24964545667171478,7652,184,10,1986.9823587992603,1950.8020612598727,0.03742735375823617
+pancreas,Epsilon,raw_u_s_ratio,142,3,0.24828124046325684,-0.007834852673113346,0.2561160931363702,7643,182,10,1987.4883886593532,1950.8020612598727,0.04188794735377935
+pancreas,Epsilon,unspliced_only,142,2,0.5162808895111084,0.037897709757089615,0.4783831797540188,7665,86,8,2008.7439384979302,1950.8020612598727,0.0021621058785918517
+pancreas,Ngn3 high EP,scPTR_gamma,642,2,0.2595919966697693,0.20570549368858337,0.05388650298118591,6715,166,14,1959.811815840309,1950.8020612598727,0.2251093567475838
+pancreas,Ngn3 high EP,raw_u_s_ratio,642,2,0.27136391401290894,0.13323815166950226,0.13812576234340668,6277,144,14,1956.2610192837465,1950.8020612598727,0.2829267590563195
+pancreas,Ngn3 high EP,unspliced_only,642,3,0.39430126547813416,0.09058266133069992,0.30371860414743423,9751,172,16,1987.536063285249,1950.8020612598727,0.0220836255226513
+pancreas,Ngn3 low EP,scPTR_gamma,262,2,0.19171521067619324,0.28163471817970276,-0.08991950750350952,4955,100,8,1944.308264101443,1950.8020612598727,0.6174977883503827
+pancreas,Ngn3 low EP,raw_u_s_ratio,262,3,0.15234625339508057,0.06291858851909637,0.08942766487598419,4857,104,8,1941.013178467724,1950.8020612598727,0.7039838806805572
+pancreas,Ngn3 low EP,unspliced_only,262,2,0.5020143985748291,0.07734054327011108,0.424673855304718,4369,100,10,1943.822071484477,1950.8020612598727,0.5944424720538997
+pancreas,Pre-endocrine,scPTR_gamma,592,2,0.14464707672595978,0.06543423235416412,0.07921284437179565,6357,186,14,1986.0719054956344,1950.8020612598727,0.06882720937789925
+pancreas,Pre-endocrine,raw_u_s_ratio,592,2,0.5315107107162476,0.0091322036460042,0.5223785070702434,5097,130,8,1988.3606418918919,1950.8020612598727,0.06339703922073579
+pancreas,Pre-endocrine,unspliced_only,592,2,0.38243651390075684,0.07795359939336777,0.30448291450738907,8349,78,6,1993.290594800599,1950.8020612598727,0.05149755806422669
+dentate_gyrus,Astrocytes,scPTR_gamma,120,2,0.2718518078327179,0.22610591351985931,0.04574589431285858,1145,134,4,2152.1614730878186,2125.793223819302,0.6404205396778478
+dentate_gyrus,Astrocytes,raw_u_s_ratio,120,3,0.21882592141628265,0.24144326150417328,-0.022617340087890625,2270,166,8,2155.771713336497,2125.793223819302,0.3959659506888041
+dentate_gyrus,Astrocytes,unspliced_only,120,2,0.2726875841617584,0.22777089476585388,0.04491668939590454,2299,64,8,2217.225517890772,2125.793223819302,0.030593466084103373
+dentate_gyrus,Endothelial,scPTR_gamma,87,2,0.37147074937820435,0.6042932271957397,-0.2328224778175354,1928,226,12,2182.699281370923,2125.793223819302,0.1586675095114261
+dentate_gyrus,Endothelial,raw_u_s_ratio,87,2,0.4773367643356323,0.6042932271957397,-0.12695646286010742,1926,226,12,2182.9596015495295,2125.793223819302,0.15965432036907723
+dentate_gyrus,Endothelial,unspliced_only,87,2,0.44974276423454285,0.09144742041826248,0.35829534381628036,3848,170,12,2205.288907753254,2125.793223819302,0.028171286187246108
+dentate_gyrus,GABA,scPTR_gamma,61,3,0.25070151686668396,0.23518596589565277,0.015515550971031189,3101,200,12,2184.0817610062895,2125.793223819302,0.12072978317948108
+dentate_gyrus,GABA,raw_u_s_ratio,61,3,0.2706594169139862,0.2390575408935547,0.03160187602043152,3063,204,12,2173.2028985507245,2125.793223819302,0.15798535084874127
+dentate_gyrus,GABA,unspliced_only,61,3,0.34033775329589844,0.14795465767383575,0.19238309562206268,3459,156,12,2171.4265402843603,2125.793223819302,0.18264205346500545
+dentate_gyrus,Granule immature,scPTR_gamma,785,2,0.21781763434410095,0.0044475034810602665,0.21337013086304069,1379,186,12,2069.4909234412,2125.793223819302,0.7228625775919436
+dentate_gyrus,Granule immature,raw_u_s_ratio,785,2,0.21963761746883392,0.0044475034810602665,0.21519011398777366,1379,186,12,2069.4909234412,2125.793223819302,0.7228625775919436
+dentate_gyrus,Granule immature,unspliced_only,785,2,0.4359748065471649,0.28314903378486633,0.15282577276229858,3932,146,12,2148.885323660714,2125.793223819302,0.3311485755338192
+dentate_gyrus,Granule mature,scPTR_gamma,1070,3,0.14221437275409698,-0.041013121604919434,0.18322749435901642,2068,122,12,2200.1423319327732,2125.793223819302,0.17418419988843048
+dentate_gyrus,Granule mature,raw_u_s_ratio,1070,3,0.14217877388000488,-0.042544618248939514,0.1847233921289444,2240,110,10,2167.970460048426,2125.793223819302,0.26058862237580505
+dentate_gyrus,Granule mature,unspliced_only,1070,3,0.20791801810264587,0.11945679783821106,0.08846122026443481,4673,158,12,2138.2077769969546,2125.793223819302,0.3468520183707841
+dentate_gyrus,Microglia,scPTR_gamma,81,2,0.3429003059864044,0.03673490881919861,0.3061653971672058,1039,96,10,2260.1787190082646,2125.793223819302,0.020939834669401306
+dentate_gyrus,Microglia,raw_u_s_ratio,81,2,0.3610897660255432,0.12908099591732025,0.23200877010822296,608,142,10,1993.3015873015872,2125.793223819302,0.969779455327401
+dentate_gyrus,Microglia,unspliced_only,81,3,0.4434473514556885,0.23677559196949005,0.20667175948619843,2574,186,12,2307.4949622166246,2125.793223819302,0.0007932208003180938
+dentate_gyrus,Mossy,scPTR_gamma,75,3,0.27764201164245605,0.21529963612556458,0.06234237551689148,3012,98,6,2097.40886167147,2125.793223819302,0.6501519616027347
+dentate_gyrus,Mossy,raw_u_s_ratio,75,2,0.4245051145553589,0.13250452280044556,0.29200059175491333,1218,76,8,2081.905777777778,2125.793223819302,0.6874454916494552
+dentate_gyrus,Mossy,unspliced_only,75,2,0.48850250244140625,0.2958618998527527,0.19264060258865356,3018,114,12,2163.257184430702,2125.793223819302,0.17533616653974776
+dentate_gyrus,Neuroblast,scPTR_gamma,417,2,0.3079949915409088,0.32819610834121704,-0.020201116800308228,2951,166,10,2154.1149045521292,2125.793223819302,0.191766510004646
+dentate_gyrus,Neuroblast,raw_u_s_ratio,417,2,0.5127217769622803,0.28867948055267334,0.22404229640960693,2796,146,12,2139.602633617351,2125.793223819302,0.3502169658004279
+dentate_gyrus,Neuroblast,unspliced_only,417,2,0.30622172355651855,0.35018080472946167,-0.043959081172943115,3927,136,12,2137.7159154145797,2125.793223819302,0.3749809196340925
+dentate_gyrus,OL,scPTR_gamma,50,2,0.3665846586227417,0.1421527862548828,0.2244318723678589,1354,42,6,2333.402689873418,2125.793223819302,0.0016200248962954219
+dentate_gyrus,OL,raw_u_s_ratio,50,2,0.26753032207489014,0.1421527862548828,0.12537753582000732,1360,38,6,2331.784251968504,2125.793223819302,0.0014728785128519262
+dentate_gyrus,OL,unspliced_only,50,2,0.534844160079956,0.24209313094615936,0.2927510291337967,2100,102,12,2384.0226221079693,2125.793223819302,6.428967723741294e-08
+dentate_gyrus,OPC,scPTR_gamma,53,2,0.3932024836540222,0.17364031076431274,0.21956217288970947,1012,14,4,2233.8670157068063,2125.793223819302,0.2601786601709334
+dentate_gyrus,OPC,raw_u_s_ratio,53,2,0.33244553208351135,0.17718559503555298,0.15525993704795837,1068,20,4,2207.5555555555557,2125.793223819302,0.34316186894633194
+dentate_gyrus,Radial Glia-like,scPTR_gamma,51,2,0.3118036091327667,0.027165990322828293,0.28463761880993843,146,0,0,2082.2624113475176,2125.793223819302,0.6478332101393478
+dentate_gyrus,Radial Glia-like,raw_u_s_ratio,51,2,0.20574317872524261,0.027165990322828293,0.17857718840241432,133,0,0,2087.2,2125.793223819302,0.6635062058661867
+dentate_gyrus,Radial Glia-like,unspliced_only,51,2,0.2914108335971832,0.18258264660835266,0.10882818698883057,1783,38,4,2210.9969474969475,2125.793223819302,0.039140414174654435

output/comprehensive_fixes/results/coherence_ablation.json

@@ -0,0 +1,26 @@
+{
+  "n_clusters_tested": 19,
+  "summary_by_method": {
+    "scPTR_gamma": {
+      "n_clusters": 19,
+      "mean_invisibility": 0.08081366305582617,
+      "total_sig_pathways": 2622,
+      "total_expected_pathways": 180,
+      "mean_diff_genes": 3719.157894736842
+    },
+    "raw_u_s_ratio": {
+      "n_clusters": 19,
+      "mean_invisibility": 0.15686803808631866,
+      "total_sig_pathways": 2372,
+      "total_expected_pathways": 168,
+      "mean_diff_genes": 3388.4736842105262
+    },
+    "unspliced_only": {
+      "n_clusters": 18,
+      "mean_invisibility": 0.25947572973867256,
+      "total_sig_pathways": 2258,
+      "total_expected_pathways": 192,
+      "mean_diff_genes": 5208.888888888889
+    }
+  }
+}

output/comprehensive_fixes/results/coherence_ablation_pathways.csv

@@ -0,0 +1,271 @@
+dataset,cluster,method,pathway
+pancreas,Alpha,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Alpha,scPTR_gamma,Autophagy
+pancreas,Alpha,scPTR_gamma,Thermogenesis
+pancreas,Alpha,scPTR_gamma,Non-alcoholic fatty liver disease (NAFLD)
+pancreas,Alpha,scPTR_gamma,Huntington disease
+pancreas,Alpha,raw_u_s_ratio,Spliceosome
+pancreas,Alpha,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Alpha,raw_u_s_ratio,RNA transport
+pancreas,Alpha,raw_u_s_ratio,Thermogenesis
+pancreas,Alpha,raw_u_s_ratio,Proteasome
+pancreas,Alpha,unspliced_only,Autophagy
+pancreas,Alpha,unspliced_only,Spliceosome
+pancreas,Alpha,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Alpha,unspliced_only,Inositol phosphate metabolism
+pancreas,Alpha,unspliced_only,Phosphatidylinositol signaling system
+pancreas,Beta,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Beta,scPTR_gamma,Thermogenesis
+pancreas,Beta,scPTR_gamma,Autophagy
+pancreas,Beta,scPTR_gamma,Ubiquitin mediated proteolysis
+pancreas,Beta,scPTR_gamma,Alzheimer disease
+pancreas,Beta,raw_u_s_ratio,Ubiquitin mediated proteolysis
+pancreas,Beta,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Beta,raw_u_s_ratio,RNA transport
+pancreas,Beta,raw_u_s_ratio,Spliceosome
+pancreas,Beta,raw_u_s_ratio,Thermogenesis
+pancreas,Beta,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Beta,unspliced_only,Autophagy
+pancreas,Beta,unspliced_only,Phosphatidylinositol signaling system
+pancreas,Beta,unspliced_only,RNA transport
+pancreas,Beta,unspliced_only,Thermogenesis
+pancreas,Delta,scPTR_gamma,Autophagy
+pancreas,Delta,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Delta,scPTR_gamma,RNA transport
+pancreas,Delta,scPTR_gamma,Spliceosome
+pancreas,Delta,scPTR_gamma,Mitophagy
+pancreas,Delta,raw_u_s_ratio,Autophagy
+pancreas,Delta,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Delta,raw_u_s_ratio,RNA transport
+pancreas,Delta,raw_u_s_ratio,Spliceosome
+pancreas,Delta,raw_u_s_ratio,Mitophagy
+pancreas,Delta,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Delta,unspliced_only,Autophagy
+pancreas,Delta,unspliced_only,Ubiquitin mediated proteolysis
+pancreas,Delta,unspliced_only,Spliceosome
+pancreas,Delta,unspliced_only,Bacterial invasion of epithelial cells
+pancreas,Ductal,scPTR_gamma,RNA transport
+pancreas,Ductal,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Ductal,scPTR_gamma,Nucleotide excision repair
+pancreas,Ductal,scPTR_gamma,Cell cycle
+pancreas,Ductal,scPTR_gamma,Bacterial invasion of epithelial cells
+pancreas,Ductal,raw_u_s_ratio,Cell cycle
+pancreas,Ductal,raw_u_s_ratio,RNA transport
+pancreas,Ductal,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Ductal,raw_u_s_ratio,Thermogenesis
+pancreas,Ductal,raw_u_s_ratio,Nucleotide excision repair
+pancreas,Ductal,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Ductal,unspliced_only,Cell cycle
+pancreas,Ductal,unspliced_only,Ubiquitin mediated proteolysis
+pancreas,Ductal,unspliced_only,Huntington disease
+pancreas,Ductal,unspliced_only,Non-small cell lung cancer
+pancreas,Epsilon,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Epsilon,scPTR_gamma,Thermogenesis
+pancreas,Epsilon,scPTR_gamma,RNA transport
+pancreas,Epsilon,scPTR_gamma,Autophagy
+pancreas,Epsilon,scPTR_gamma,Alzheimer disease
+pancreas,Epsilon,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Epsilon,raw_u_s_ratio,Thermogenesis
+pancreas,Epsilon,raw_u_s_ratio,RNA transport
+pancreas,Epsilon,raw_u_s_ratio,Alzheimer disease
+pancreas,Epsilon,raw_u_s_ratio,Autophagy
+pancreas,Epsilon,unspliced_only,Autophagy
+pancreas,Epsilon,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Epsilon,unspliced_only,RNA transport
+pancreas,Epsilon,unspliced_only,Thermogenesis
+pancreas,Epsilon,unspliced_only,Thyroid hormone signaling pathway
+pancreas,Ngn3 high EP,scPTR_gamma,RNA transport
+pancreas,Ngn3 high EP,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Ngn3 high EP,scPTR_gamma,Ubiquitin mediated proteolysis
+pancreas,Ngn3 high EP,scPTR_gamma,Chronic myeloid leukemia
+pancreas,Ngn3 high EP,scPTR_gamma,Huntington disease
+pancreas,Ngn3 high EP,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Ngn3 high EP,raw_u_s_ratio,Ubiquitin mediated proteolysis
+pancreas,Ngn3 high EP,raw_u_s_ratio,Spliceosome
+pancreas,Ngn3 high EP,raw_u_s_ratio,Thermogenesis
+pancreas,Ngn3 high EP,raw_u_s_ratio,Autophagy
+pancreas,Ngn3 high EP,unspliced_only,Autophagy
+pancreas,Ngn3 high EP,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Ngn3 high EP,unspliced_only,Ubiquitin mediated proteolysis
+pancreas,Ngn3 high EP,unspliced_only,Bacterial invasion of epithelial cells
+pancreas,Ngn3 high EP,unspliced_only,Axon guidance
+pancreas,Ngn3 low EP,scPTR_gamma,RNA transport
+pancreas,Ngn3 low EP,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Ngn3 low EP,scPTR_gamma,Spliceosome
+pancreas,Ngn3 low EP,scPTR_gamma,Cell cycle
+pancreas,Ngn3 low EP,scPTR_gamma,Thermogenesis
+pancreas,Ngn3 low EP,raw_u_s_ratio,RNA transport
+pancreas,Ngn3 low EP,raw_u_s_ratio,Thermogenesis
+pancreas,Ngn3 low EP,raw_u_s_ratio,Spliceosome
+pancreas,Ngn3 low EP,raw_u_s_ratio,Cell cycle
+pancreas,Ngn3 low EP,raw_u_s_ratio,Nucleotide excision repair
+pancreas,Ngn3 low EP,unspliced_only,Bacterial invasion of epithelial cells
+pancreas,Ngn3 low EP,unspliced_only,Cell cycle
+pancreas,Ngn3 low EP,unspliced_only,Pancreatic cancer
+pancreas,Ngn3 low EP,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Ngn3 low EP,unspliced_only,Chronic myeloid leukemia
+pancreas,Pre-endocrine,scPTR_gamma,Autophagy
+pancreas,Pre-endocrine,scPTR_gamma,Protein processing in endoplasmic reticulum
+pancreas,Pre-endocrine,scPTR_gamma,Huntington disease
+pancreas,Pre-endocrine,scPTR_gamma,Thermogenesis
+pancreas,Pre-endocrine,scPTR_gamma,Oxidative phosphorylation
+pancreas,Pre-endocrine,raw_u_s_ratio,Protein processing in endoplasmic reticulum
+pancreas,Pre-endocrine,raw_u_s_ratio,RNA transport
+pancreas,Pre-endocrine,raw_u_s_ratio,Spliceosome
+pancreas,Pre-endocrine,raw_u_s_ratio,Alzheimer disease
+pancreas,Pre-endocrine,raw_u_s_ratio,Renal cell carcinoma
+pancreas,Pre-endocrine,unspliced_only,Protein processing in endoplasmic reticulum
+pancreas,Pre-endocrine,unspliced_only,Mitophagy
+pancreas,Pre-endocrine,unspliced_only,Huntington disease
+pancreas,Pre-endocrine,unspliced_only,Autophagy
+pancreas,Pre-endocrine,unspliced_only,ErbB signaling pathway
+dentate_gyrus,Astrocytes,scPTR_gamma,Huntington disease
+dentate_gyrus,Astrocytes,scPTR_gamma,Ribosome
+dentate_gyrus,Astrocytes,scPTR_gamma,Thermogenesis
+dentate_gyrus,Astrocytes,scPTR_gamma,Oxidative phosphorylation
+dentate_gyrus,Astrocytes,scPTR_gamma,Parkinson disease
+dentate_gyrus,Astrocytes,raw_u_s_ratio,Oxidative phosphorylation
+dentate_gyrus,Astrocytes,raw_u_s_ratio,Huntington disease
+dentate_gyrus,Astrocytes,raw_u_s_ratio,Parkinson disease
+dentate_gyrus,Astrocytes,raw_u_s_ratio,Thermogenesis
+dentate_gyrus,Astrocytes,raw_u_s_ratio,Alzheimer disease
+dentate_gyrus,Astrocytes,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,Astrocytes,unspliced_only,Huntington disease
+dentate_gyrus,Astrocytes,unspliced_only,Parkinson disease
+dentate_gyrus,Astrocytes,unspliced_only,Alzheimer disease
+dentate_gyrus,Astrocytes,unspliced_only,Thermogenesis
+dentate_gyrus,Endothelial,scPTR_gamma,Ubiquitin mediated proteolysis
+dentate_gyrus,Endothelial,scPTR_gamma,Ribosome
+dentate_gyrus,Endothelial,scPTR_gamma,Chronic myeloid leukemia
+dentate_gyrus,Endothelial,scPTR_gamma,Choline metabolism in cancer
+dentate_gyrus,Endothelial,scPTR_gamma,Long-term potentiation
+dentate_gyrus,Endothelial,raw_u_s_ratio,Ubiquitin mediated proteolysis
+dentate_gyrus,Endothelial,raw_u_s_ratio,Ribosome
+dentate_gyrus,Endothelial,raw_u_s_ratio,Chronic myeloid leukemia
+dentate_gyrus,Endothelial,raw_u_s_ratio,Choline metabolism in cancer
+dentate_gyrus,Endothelial,raw_u_s_ratio,Long-term potentiation
+dentate_gyrus,Endothelial,unspliced_only,Huntington disease
+dentate_gyrus,Endothelial,unspliced_only,Retrograde endocannabinoid signaling
+dentate_gyrus,Endothelial,unspliced_only,Alzheimer disease
+dentate_gyrus,Endothelial,unspliced_only,Axon guidance
+dentate_gyrus,Endothelial,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,GABA,scPTR_gamma,Retrograde endocannabinoid signaling
+dentate_gyrus,GABA,scPTR_gamma,Oxidative phosphorylation
+dentate_gyrus,GABA,scPTR_gamma,Huntington disease
+dentate_gyrus,GABA,scPTR_gamma,Alzheimer disease
+dentate_gyrus,GABA,scPTR_gamma,Long-term potentiation
+dentate_gyrus,GABA,raw_u_s_ratio,Oxidative phosphorylation
+dentate_gyrus,GABA,raw_u_s_ratio,Retrograde endocannabinoid signaling
+dentate_gyrus,GABA,raw_u_s_ratio,Alzheimer disease
+dentate_gyrus,GABA,raw_u_s_ratio,Huntington disease
+dentate_gyrus,GABA,raw_u_s_ratio,Thermogenesis
+dentate_gyrus,GABA,unspliced_only,Huntington disease
+dentate_gyrus,GABA,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,GABA,unspliced_only,Alzheimer disease
+dentate_gyrus,GABA,unspliced_only,Axon guidance
+dentate_gyrus,GABA,unspliced_only,Thermogenesis
+dentate_gyrus,Granule immature,scPTR_gamma,Huntington disease
+dentate_gyrus,Granule immature,scPTR_gamma,Parkinson disease
+dentate_gyrus,Granule immature,scPTR_gamma,Retrograde endocannabinoid signaling
+dentate_gyrus,Granule immature,scPTR_gamma,Long-term potentiation
+dentate_gyrus,Granule immature,scPTR_gamma,Long-term depression
+dentate_gyrus,Granule immature,raw_u_s_ratio,Huntington disease
+dentate_gyrus,Granule immature,raw_u_s_ratio,Parkinson disease
+dentate_gyrus,Granule immature,raw_u_s_ratio,Retrograde endocannabinoid signaling
+dentate_gyrus,Granule immature,raw_u_s_ratio,Long-term potentiation
+dentate_gyrus,Granule immature,raw_u_s_ratio,Long-term depression
+dentate_gyrus,Granule immature,unspliced_only,Retrograde endocannabinoid signaling
+dentate_gyrus,Granule immature,unspliced_only,Huntington disease
+dentate_gyrus,Granule immature,unspliced_only,Long-term potentiation
+dentate_gyrus,Granule immature,unspliced_only,Alzheimer disease
+dentate_gyrus,Granule immature,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,Granule mature,scPTR_gamma,Alzheimer disease
+dentate_gyrus,Granule mature,scPTR_gamma,Spliceosome
+dentate_gyrus,Granule mature,scPTR_gamma,Huntington disease
+dentate_gyrus,Granule mature,scPTR_gamma,Ubiquitin mediated proteolysis
+dentate_gyrus,Granule mature,scPTR_gamma,Oxidative phosphorylation
+dentate_gyrus,Granule mature,raw_u_s_ratio,Alzheimer disease
+dentate_gyrus,Granule mature,raw_u_s_ratio,Huntington disease
+dentate_gyrus,Granule mature,raw_u_s_ratio,Ubiquitin mediated proteolysis
+dentate_gyrus,Granule mature,raw_u_s_ratio,Spliceosome
+dentate_gyrus,Granule mature,raw_u_s_ratio,Ribosome
+dentate_gyrus,Granule mature,unspliced_only,Huntington disease
+dentate_gyrus,Granule mature,unspliced_only,Thermogenesis
+dentate_gyrus,Granule mature,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,Granule mature,unspliced_only,Alzheimer disease
+dentate_gyrus,Granule mature,unspliced_only,Parkinson disease
+dentate_gyrus,Microglia,scPTR_gamma,Alzheimer disease
+dentate_gyrus,Microglia,scPTR_gamma,Long-term potentiation
+dentate_gyrus,Microglia,scPTR_gamma,Glutamatergic synapse
+dentate_gyrus,Microglia,scPTR_gamma,Dopaminergic synapse
+dentate_gyrus,Microglia,scPTR_gamma,Retrograde endocannabinoid signaling
+dentate_gyrus,Microglia,raw_u_s_ratio,Ribosome
+dentate_gyrus,Microglia,raw_u_s_ratio,Long-term potentiation
+dentate_gyrus,Microglia,raw_u_s_ratio,Renal cell carcinoma
+dentate_gyrus,Microglia,raw_u_s_ratio,Rap1 signaling pathway
+dentate_gyrus,Microglia,raw_u_s_ratio,Ras signaling pathway
+dentate_gyrus,Microglia,unspliced_only,Retrograde endocannabinoid signaling
+dentate_gyrus,Microglia,unspliced_only,Ribosome
+dentate_gyrus,Microglia,unspliced_only,Long-term potentiation
+dentate_gyrus,Microglia,unspliced_only,Axon guidance
+dentate_gyrus,Microglia,unspliced_only,Circadian entrainment
+dentate_gyrus,Mossy,scPTR_gamma,Thermogenesis
+dentate_gyrus,Mossy,scPTR_gamma,Ribosome
+dentate_gyrus,Mossy,scPTR_gamma,Huntington disease
+dentate_gyrus,Mossy,scPTR_gamma,Parkinson disease
+dentate_gyrus,Mossy,scPTR_gamma,Alzheimer disease
+dentate_gyrus,Mossy,raw_u_s_ratio,Thermogenesis
+dentate_gyrus,Mossy,raw_u_s_ratio,mRNA surveillance pathway
+dentate_gyrus,Mossy,raw_u_s_ratio,RNA transport
+dentate_gyrus,Mossy,raw_u_s_ratio,cAMP signaling pathway
+dentate_gyrus,Mossy,raw_u_s_ratio,Long-term potentiation
+dentate_gyrus,Mossy,unspliced_only,Huntington disease
+dentate_gyrus,Mossy,unspliced_only,Ribosome
+dentate_gyrus,Mossy,unspliced_only,Alzheimer disease
+dentate_gyrus,Mossy,unspliced_only,Retrograde endocannabinoid signaling
+dentate_gyrus,Mossy,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,Neuroblast,scPTR_gamma,Alzheimer disease
+dentate_gyrus,Neuroblast,scPTR_gamma,Long-term potentiation
+dentate_gyrus,Neuroblast,scPTR_gamma,Retrograde endocannabinoid signaling
+dentate_gyrus,Neuroblast,scPTR_gamma,Spliceosome
+dentate_gyrus,Neuroblast,scPTR_gamma,Huntington disease
+dentate_gyrus,Neuroblast,raw_u_s_ratio,Retrograde endocannabinoid signaling
+dentate_gyrus,Neuroblast,raw_u_s_ratio,Long-term potentiation
+dentate_gyrus,Neuroblast,raw_u_s_ratio,Alzheimer disease
+dentate_gyrus,Neuroblast,raw_u_s_ratio,Thermogenesis
+dentate_gyrus,Neuroblast,raw_u_s_ratio,Spliceosome
+dentate_gyrus,Neuroblast,unspliced_only,Retrograde endocannabinoid signaling
+dentate_gyrus,Neuroblast,unspliced_only,Thermogenesis
+dentate_gyrus,Neuroblast,unspliced_only,Ribosome
+dentate_gyrus,Neuroblast,unspliced_only,Huntington disease
+dentate_gyrus,Neuroblast,unspliced_only,Oxidative phosphorylation
+dentate_gyrus,OL,scPTR_gamma,Ribosome
+dentate_gyrus,OL,scPTR_gamma,Huntington disease
+dentate_gyrus,OL,scPTR_gamma,Long-term potentiation
+dentate_gyrus,OL,scPTR_gamma,Retrograde endocannabinoid signaling
+dentate_gyrus,OL,scPTR_gamma,Endocytosis
+dentate_gyrus,OL,raw_u_s_ratio,Ribosome
+dentate_gyrus,OL,raw_u_s_ratio,Huntington disease
+dentate_gyrus,OL,raw_u_s_ratio,Long-term potentiation
+dentate_gyrus,OL,raw_u_s_ratio,Retrograde endocannabinoid signaling
+dentate_gyrus,OL,raw_u_s_ratio,Endocytosis
+dentate_gyrus,OL,unspliced_only,Retrograde endocannabinoid signaling
+dentate_gyrus,OL,unspliced_only,Long-term potentiation
+dentate_gyrus,OL,unspliced_only,Long-term depression
+dentate_gyrus,OL,unspliced_only,Alzheimer disease
+dentate_gyrus,OL,unspliced_only,Huntington disease
+dentate_gyrus,OPC,scPTR_gamma,Spliceosome
+dentate_gyrus,OPC,scPTR_gamma,Ribosome
+dentate_gyrus,OPC,scPTR_gamma,Thermogenesis
+dentate_gyrus,OPC,scPTR_gamma,Axon guidance
+dentate_gyrus,OPC,scPTR_gamma,Oxidative phosphorylation
+dentate_gyrus,OPC,raw_u_s_ratio,Spliceosome
+dentate_gyrus,OPC,raw_u_s_ratio,Ribosome
+dentate_gyrus,OPC,raw_u_s_ratio,Oxidative phosphorylation
+dentate_gyrus,OPC,raw_u_s_ratio,Axon guidance
+dentate_gyrus,OPC,raw_u_s_ratio,Thermogenesis
+dentate_gyrus,Radial Glia-like,unspliced_only,RNA transport
+dentate_gyrus,Radial Glia-like,unspliced_only,Huntington disease
+dentate_gyrus,Radial Glia-like,unspliced_only,Ribosome
+dentate_gyrus,Radial Glia-like,unspliced_only,Protein processing in endoplasmic reticulum
+dentate_gyrus,Radial Glia-like,unspliced_only,Oxidative phosphorylation

output/comprehensive_fixes/results/hub_consistency.json

@@ -0,0 +1,179 @@
+{
+  "pairwise_correlations": [
+    {
+      "dataset_a": "dentate_gyrus",
+      "dataset_b": "neuroblastoma",
+      "spearman_r": 0.6207522318391883,
+      "spearman_p": 0.07443796489097941,
+      "n_shared": 9
+    },
+    {
+      "dataset_a": "dentate_gyrus",
+      "dataset_b": "pancreas",
+      "spearman_r": 0.34788117561515225,
+      "spearman_p": 0.17122073706262758,
+      "n_shared": 17
+    },
+    {
+      "dataset_a": "neuroblastoma",
+      "dataset_b": "pancreas",
+      "spearman_r": 0.6906864796671202,
+      "spearman_p": 0.012888876660556747,
+      "n_shared": 12
+    }
+  ],
+  "universal_hubs": [
+    {
+      "rbp": "YBX1",
+      "n_datasets_top20": 3,
+      "datasets": "dentate_gyrus, neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 550,
+      "targets_neuroblastoma": 21,
+      "targets_pancreas": 158
+    },
+    {
+      "rbp": "FUS",
+      "n_datasets_top20": 2,
+      "datasets": "neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 0,
+      "targets_neuroblastoma": 14,
+      "targets_pancreas": 32
+    },
+    {
+      "rbp": "HNRNPA1",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 209,
+      "targets_neuroblastoma": 0,
+      "targets_pancreas": 166
+    },
+    {
+      "rbp": "HNRNPA2B1",
+      "n_datasets_top20": 2,
+      "datasets": "neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 0,
+      "targets_neuroblastoma": 46,
+      "targets_pancreas": 12
+    },
+    {
+      "rbp": "ELAVL1",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 129,
+      "targets_neuroblastoma": 0,
+      "targets_pancreas": 43
+    },
+    {
+      "rbp": "HNRNPC",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 109,
+      "targets_neuroblastoma": 3,
+      "targets_pancreas": 29
+    },
+    {
+      "rbp": "RBFOX3",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 197,
+      "targets_neuroblastoma": 0,
+      "targets_pancreas": 70
+    },
+    {
+      "rbp": "SRSF3",
+      "n_datasets_top20": 2,
+      "datasets": "neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 0,
+      "targets_neuroblastoma": 11,
+      "targets_pancreas": 144
+    },
+    {
+      "rbp": "TRA2B",
+      "n_datasets_top20": 2,
+      "datasets": "neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 0,
+      "targets_neuroblastoma": 6,
+      "targets_pancreas": 47
+    },
+    {
+      "rbp": "MATR3",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 134,
+      "targets_neuroblastoma": 0,
+      "targets_pancreas": 27
+    },
+    {
+      "rbp": "PTBP1",
+      "n_datasets_top20": 2,
+      "datasets": "neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 0,
+      "targets_neuroblastoma": 6,
+      "targets_pancreas": 27
+    },
+    {
+      "rbp": "HNRNPD",
+      "n_datasets_top20": 2,
+      "datasets": "neuroblastoma, pancreas",
+      "targets_dentate_gyrus": 0,
+      "targets_neuroblastoma": 18,
+      "targets_pancreas": 48
+    },
+    {
+      "rbp": "ELAVL4",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 73,
+      "targets_neuroblastoma": 0,
+      "targets_pancreas": 24
+    },
+    {
+      "rbp": "STAU2",
+      "n_datasets_top20": 2,
+      "datasets": "dentate_gyrus, pancreas",
+      "targets_dentate_gyrus": 44,
+      "targets_neuroblastoma": 0,
+      "targets_pancreas": 15
+    }
+  ],
+  "dataset_hubs": {
+    "dentate_gyrus": {
+      "YBX1": 550,
+      "RBFOX1": 230,
+      "CELF2": 214,
+      "HNRNPA1": 209,
+      "RBFOX3": 197,
+      "ELAVL3": 194,
+      "RBFOX2": 143,
+      "MATR3": 134,
+      "ELAVL1": 129,
+      "MBNL2": 118
+    },
+    "neuroblastoma": {
+      "HNRNPA2B1": 46,
+      "PABPC1": 28,
+      "YBX1": 21,
+      "HNRNPD": 18,
+      "HNRNPU": 18,
+      "PRPF8": 17,
+      "SNRNP200": 16,
+      "FUS": 14,
+      "HNRNPK": 14,
+      "NCL": 12
+    },
+    "pancreas": {
+      "HNRNPA1": 166,
+      "YBX1": 158,
+      "SRSF3": 144,
+      "RBFOX3": 70,
+      "HNRNPD": 48,
+      "TRA2B": 47,
+      "ELAVL1": 43,
+      "FUS": 32,
+      "SRSF1": 30,
+      "ZFP36L1": 30
+    }
+  },
+  "n_universal": 14,
+  "n_tissue_specific": 31
+}

output/comprehensive_fixes/results/hub_consistency_table.csv

@@ -0,0 +1,46 @@
+rbp,n_datasets_top20,datasets,targets_dentate_gyrus,targets_neuroblastoma,targets_pancreas
+YBX1,3,"dentate_gyrus, neuroblastoma, pancreas",550,21,158
+FUS,2,"neuroblastoma, pancreas",0,14,32
+HNRNPA1,2,"dentate_gyrus, pancreas",209,0,166
+HNRNPA2B1,2,"neuroblastoma, pancreas",0,46,12
+ELAVL1,2,"dentate_gyrus, pancreas",129,0,43
+HNRNPC,2,"dentate_gyrus, pancreas",109,3,29
+RBFOX3,2,"dentate_gyrus, pancreas",197,0,70
+SRSF3,2,"neuroblastoma, pancreas",0,11,144
+TRA2B,2,"neuroblastoma, pancreas",0,6,47
+MATR3,2,"dentate_gyrus, pancreas",134,0,27
+PTBP1,2,"neuroblastoma, pancreas",0,6,27
+HNRNPD,2,"neuroblastoma, pancreas",0,18,48
+ELAVL4,2,"dentate_gyrus, pancreas",73,0,24
+STAU2,2,"dentate_gyrus, pancreas",44,0,15
+EWSR1,1,neuroblastoma,0,8,0
+FTO,1,dentate_gyrus,80,0,0
+ELAVL3,1,dentate_gyrus,194,1,0
+AGO2,1,dentate_gyrus,63,0,6
+CELF1,1,dentate_gyrus,102,0,0
+CELF2,1,dentate_gyrus,214,0,8
+DDX5,1,neuroblastoma,0,4,0
+MBNL1,1,pancreas,28,0,16
+MBNL2,1,dentate_gyrus,118,1,8
+MSI1,1,pancreas,35,0,21
+HNRNPM,1,neuroblastoma,0,6,0
+HNRNPU,1,neuroblastoma,0,18,0
+IGF2BP1,1,pancreas,0,0,11
+KHDRBS1,1,dentate_gyrus,55,1,0
+HNRNPK,1,neuroblastoma,0,14,0
+PTBP2,1,dentate_gyrus,64,0,7
+PRPF8,1,neuroblastoma,0,17,0
+PABPC1,1,neuroblastoma,0,28,0
+NCL,1,neuroblastoma,0,12,0
+METTL3,1,pancreas,8,0,11
+PUM1,1,dentate_gyrus,58,0,0
+RBFOX1,1,dentate_gyrus,230,2,8
+QKI,1,neuroblastoma,0,6,0
+SRSF1,1,pancreas,0,0,30
+SNRPA,1,neuroblastoma,0,7,0
+SNRNP200,1,neuroblastoma,0,16,0
+RBFOX2,1,dentate_gyrus,143,4,0
+SRSF7,1,neuroblastoma,0,10,0
+SRSF10,1,neuroblastoma,0,5,0
+TIA1,1,dentate_gyrus,74,0,0
+ZFP36L1,1,pancreas,0,0,30

output/comprehensive_fixes/results/nb_specific_depmap.json

@@ -0,0 +1,50 @@
+{
+  "neuroblastoma": {
+    "n_hub_rbps": 20,
+    "n_hub_matched": 20,
+    "n_nonhub_matched": 28,
+    "nb_hub_mean_dep": -1.1231941630752047,
+    "nb_nonhub_mean_dep": -0.6345991668039,
+    "nb_mw_p": 0.024066198109790972,
+    "all_hub_mean_dep": -1.1200964888610585,
+    "all_nonhub_mean_dep": -0.6168147386880988,
+    "all_mw_p": 0.02072830347215501,
+    "nb_specificity_p": 0.5269580116874888,
+    "hub_nb_mean": -1.1231941630752047,
+    "hub_non_nb_mean": -1.1199911625364276,
+    "ntargets_dep_spearman_r": -0.2594713478934196,
+    "ntargets_dep_spearman_p": 0.07492474053632316
+  },
+  "pancreas": {
+    "n_hub_rbps": 20,
+    "n_hub_matched": 20,
+    "n_nonhub_matched": 137,
+    "nb_hub_mean_dep": -0.9730124214105149,
+    "nb_nonhub_mean_dep": -0.49625922530249783,
+    "nb_mw_p": 0.006820384207358076,
+    "all_hub_mean_dep": -0.9997965508106808,
+    "all_nonhub_mean_dep": -0.4898479613026557,
+    "all_mw_p": 0.004014393322680695,
+    "nb_specificity_p": 0.5697845131323614,
+    "hub_nb_mean": -0.9730124214105149,
+    "hub_non_nb_mean": -1.0005145334334458,
+    "ntargets_dep_spearman_r": -0.09211910713859293,
+    "ntargets_dep_spearman_p": 0.2511886468436864
+  },
+  "dentate_gyrus": {
+    "n_hub_rbps": 20,
+    "n_hub_matched": 20,
+    "n_nonhub_matched": 27,
+    "nb_hub_mean_dep": -0.7164812943730803,
+    "nb_nonhub_mean_dep": -0.3771843463296336,
+    "nb_mw_p": 0.0893471950344088,
+    "all_hub_mean_dep": -0.6933051686072866,
+    "all_nonhub_mean_dep": -0.3742576462007085,
+    "all_mw_p": 0.13860968767464932,
+    "nb_specificity_p": 0.5377136358338882,
+    "hub_nb_mean": -0.7164812943730803,
+    "hub_non_nb_mean": -0.6923244154397531,
+    "ntargets_dep_spearman_r": -0.2586847838682696,
+    "ntargets_dep_spearman_p": 0.07913620588500175
+  }
+}

output/comprehensive_fixes/results/per_cell_scifate.json

@@ -0,0 +1,14 @@
+{
+  "n_cells_total": 7404,
+  "n_cells_valid": 7403,
+  "mean_gamma_corr": 0.6400740651477818,
+  "mean_raw_corr": 0.6372983859554561,
+  "median_gamma_corr": 0.6462974763496186,
+  "median_raw_corr": 0.6410144251697661,
+  "wilcoxon_p": 1.0308648272252094e-297,
+  "gamma_better_frac": 0.7224098338511414,
+  "raw_better_frac": 0.27759016614885856,
+  "mean_gamma_cv": 3.524893548703429,
+  "mean_raw_cv": 1.2779634798135078,
+  "cv_wilcoxon_p": 1.0
+}

output/comprehensive_fixes/results/utr_network_validation.json

@@ -0,0 +1,47 @@
+{
+  "pancreas": {
+    "dataset": "pancreas",
+    "n_targets": 176,
+    "n_matched": 166,
+    "utr_length_destab_median": 2420.0,
+    "utr_length_stab_median": 2432.0,
+    "utr_length_mw_p": 0.6757002839765559,
+    "au_content_destab_median": 0.576214405360134,
+    "au_content_stab_median": 0.5984087102177554,
+    "au_content_mw_p": 0.9793488740930798,
+    "spearman_r_vs_utr_length": -0.136319961802761,
+    "spearman_p_vs_utr_length": 0.07989891535893835,
+    "spearman_r_vs_au_content": -0.15385614313541593,
+    "spearman_p_vs_au_content": 0.04780261384186119
+  },
+  "dentate_gyrus": {
+    "dataset": "dentate_gyrus",
+    "n_targets": 124,
+    "n_matched": 118,
+    "utr_length_destab_median": 2522.5,
+    "utr_length_stab_median": 1965.0,
+    "utr_length_mw_p": 0.02493904657469992,
+    "au_content_destab_median": 0.5893077940041419,
+    "au_content_stab_median": 0.5942052381868609,
+    "au_content_mw_p": 0.4760398682988743,
+    "spearman_r_vs_utr_length": 0.12453139579705842,
+    "spearman_p_vs_utr_length": 0.1790799103865216,
+    "spearman_r_vs_au_content": -0.04015426248726348,
+    "spearman_p_vs_au_content": 0.6659465074321518
+  },
+  "neuroblastoma": {
+    "dataset": "neuroblastoma",
+    "n_targets": 85,
+    "n_matched": 81,
+    "utr_length_destab_median": 4230.5,
+    "utr_length_stab_median": 3594.0,
+    "utr_length_mw_p": 0.1277627029361753,
+    "au_content_destab_median": 0.6261289733287869,
+    "au_content_stab_median": 0.6113207547169811,
+    "au_content_mw_p": 0.2840004975109969,
+    "spearman_r_vs_utr_length": 0.07378048780487804,
+    "spearman_p_vs_utr_length": 0.51272750323782,
+    "spearman_r_vs_au_content": 0.12138663053297198,
+    "spearman_p_vs_au_content": 0.280366151780597
+  }
+}

output/comprehensive_improvements/results/correction_quality.json

@@ -0,0 +1,34 @@
+{
+  "neuroblastoma_raw": {
+    "dataset": "neuroblastoma",
+    "method": "raw",
+    "n_edges": 9112,
+    "n_eligible_rbps": 94,
+    "n_with_sig_go": 92,
+    "frac_with_sig_go": 0.9787234042553191
+  },
+  "neuroblastoma_corrected": {
+    "dataset": "neuroblastoma",
+    "method": "corrected",
+    "n_edges": 326,
+    "n_eligible_rbps": 12,
+    "n_with_sig_go": 12,
+    "frac_with_sig_go": 1.0
+  },
+  "pancreas_raw": {
+    "dataset": "pancreas",
+    "method": "raw",
+    "n_edges": 1112,
+    "n_eligible_rbps": 22,
+    "n_with_sig_go": 21,
+    "frac_with_sig_go": 0.9545454545454546
+  },
+  "pancreas_corrected": {
+    "dataset": "pancreas",
+    "method": "corrected",
+    "n_edges": 2198,
+    "n_eligible_rbps": 48,
+    "n_with_sig_go": 45,
+    "frac_with_sig_go": 0.9375
+  }
+}

output/comprehensive_improvements/results/gamma_advantage.json

@@ -0,0 +1,350 @@
+{
+  "pancreas": {
+    "invisible_states": {
+      "gamma_n_invisible": 2,
+      "smooth_ratio_n_invisible": 2,
+      "gamma_mean_invisibility": 0.029038458596915007,
+      "smooth_ratio_mean_invisibility": 0.04570982279255986,
+      "per_cluster": {
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+            "n_cells": "481",
+            "sil_method": 0.15257549285888672,
+            "sil_expr": 0.18451890349388123,
+            "invisibility": -0.03194341063499451,
+            "is_invisible": false
+          },
+          {
+            "cluster": "Beta",
+            "n_cells": "591",
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+            "sil_expr": 0.2098182886838913,
+            "invisibility": -0.051635026931762695,
+            "is_invisible": false
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+          {
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+            "n_cells": "70",
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+            "sil_expr": 0.13608261942863464,
+            "invisibility": 0.14072182774543762,
+            "is_invisible": false
+          },
+          {
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+            "n_cells": "916",
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+            "invisibility": -0.11830154061317444,
+            "is_invisible": false
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+          {
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+          {
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+          {
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+          },
+          {
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+          {
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+          {
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+          {
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+  },
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+            "is_invisible": false
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+          {
+            "cluster": "Neuroblast",
+            "n_cells": "417",
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+            "sil_expr": 0.32825586199760437,
+            "invisibility": -0.01910993456840515,
+            "is_invisible": false
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+          {
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+          {
+            "cluster": "Granule mature",
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+          {
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+          {
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+          {
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+          {
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+            "sil_expr": 0.014947937801480293,
+            "invisibility": 0.260152829810977,
+            "is_invisible": true
+          }
+        ]
+      }
+    },
+    "eta_squared": {
+      "gamma_wins": 3128,
+      "ratio_wins": 1203,
+      "n_genes": 4331,
+      "gamma_mean": 0.13149034679413774,
+      "ratio_mean": 0.13078642088446124,
+      "wilcoxon_p": 1.6115244882001074e-116
+    }
+  }
+}

output/comprehensive_improvements/results/go_enrichment.json

@@ -0,0 +1,994 @@
+{
+  "pancreas": {
+    "n_eligible_rbps": 48,
+    "n_with_sig_go": 45,
+    "frac_with_sig_go": 0.9375,
+    "mean_cross_rbp_jaccard": 0.047142456309122976,
+    "n_known_biology_matches": 0,
+    "concordance_hits": [],
+    "bootstrap_null_frac": 0.916,
+    "per_rbp": [
+      {
+        "rbp": "AGO2",
+        "n_targets": 21,
+        "n_sig_terms": 8,
+        "has_sig": true,
+        "top_terms": [
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)",
+          "Synapse Organization (GO:0050808)",
+          "Protein Localization To Plasma Membrane (GO:0072659)"
+        ]
+      },
+      {
+        "rbp": "AUH",
+        "n_targets": 20,
+        "n_sig_terms": 4,
+        "has_sig": true,
+        "top_terms": [
+          "Insulin Secretion (GO:0030073)",
+          "Neurotransmitter Secretion (GO:0007269)",
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)",
+          "Cellular Response To Oxidative Stress (GO:0034599)"
+        ]
+      },
+      {
+        "rbp": "CELF4",
+        "n_targets": 25,
+        "n_sig_terms": 18,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Calcium Ion Transmembrane Transporter Activity (GO:1901019)",
+          "Regulation Of Cation Channel Activity (GO:2001257)",
+          "Regulation Of Intracellular Signal Transduction (GO:1902531)",
+          "Synapse Organization (GO:0050808)",
+          "Regulation Of Voltage-Gated Calcium Channel Activity (GO:1901385)"
+        ]
+      },
+      {
+        "rbp": "CNBP",
+        "n_targets": 46,
+        "n_sig_terms": 22,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Response To Sterol (GO:0036314)",
+          "Epithelial Cell Morphogenesis (GO:0003382)",
+          "Epithelial Cell Development (GO:0002064)",
+          "Cell Morphogenesis Involved In Differentiation (GO:0000904)"
+        ]
+      },
+      {
+        "rbp": "CNOT7",
+        "n_targets": 25,
+        "n_sig_terms": 29,
+        "has_sig": true,
+        "top_terms": [
+          "Calcium Ion Import Across Plasma Membrane (GO:0098703)",
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Calcium Ion Transmembrane Transport (GO:0070588)",
+          "Calcium Ion Transmembrane Import Into Cytosol (GO:0097553)",
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)"
+        ]
+      },
+      {
+        "rbp": "DDX39B",
+        "n_targets": 21,
+        "n_sig_terms": 3,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Mitotic Cell Cycle Phase Transition (GO:1901992)",
+          "Negative Regulation Of Macromolecule Biosynthetic Process (GO:0010558)",
+          "Negative Regulation Of Cellular Biosynthetic Process (GO:0031327)"
+        ]
+      },
+      {
+        "rbp": "DDX5",
+        "n_targets": 80,
+        "n_sig_terms": 28,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Calcium Ion Transmembrane Import Into Cytosol (GO:0097553)",
+          "Calcium Ion Import Across Plasma Membrane (GO:0098703)",
+          "Response To Sterol (GO:0036314)"
+        ]
+      },
+      {
+        "rbp": "DDX6",
+        "n_targets": 27,
+        "n_sig_terms": 3,
+        "has_sig": true,
+        "top_terms": [
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Apoptotic Process (GO:0006915)"
+        ]
+      },
+      {
+        "rbp": "DICER1",
+        "n_targets": 11,
+        "n_sig_terms": 1,
+        "has_sig": true,
+        "top_terms": [
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)"
+        ]
+      },
+      {
+        "rbp": "EIF4A1",
+        "n_targets": 74,
+        "n_sig_terms": 21,
+        "has_sig": true,
+        "top_terms": [
+          "Protein Modification Process (GO:0036211)",
+          "Protein Dephosphorylation (GO:0006470)",
+          "Dephosphorylation (GO:0016311)",
+          "Purine-Containing Compound Metabolic Process (GO:0072521)",
+          "Response To Sterol (GO:0036314)"
+        ]
+      },
+      {
+        "rbp": "EIF4E",
+        "n_targets": 18,
+        "n_sig_terms": 9,
+        "has_sig": true,
+        "top_terms": [
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Synapse Assembly (GO:0007416)",
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)",
+          "Protein Dephosphorylation (GO:0006470)",
+          "Synapse Organization (GO:0050808)"
+        ]
+      },
+      {
+        "rbp": "ELAVL4",
+        "n_targets": 12,
+        "n_sig_terms": 13,
+        "has_sig": true,
+        "top_terms": [
+          "Calcium Ion Import (GO:0070509)",
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)",
+          "Positive Regulation Of Calcium Ion Transport (GO:0051928)",
+          "Positive Regulation Of Monoatomic Ion Transport (GO:0043270)",
+          "Regulation Of Heart Rate By Cardiac Conduction (GO:0086091)"
+        ]
+      },
+      {
+        "rbp": "FIP1L1",
+        "n_targets": 12,
+        "n_sig_terms": 11,
+        "has_sig": true,
+        "top_terms": [
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Potassium Ion Transport (GO:0006813)",
+          "Intracellular Monoatomic Cation Homeostasis (GO:0030003)",
+          "Regulation Of Apoptotic Process (GO:0042981)",
+          "Negative Regulation Of Intracellular Signal Transduction (GO:1902532)"
+        ]
+      },
+      {
+        "rbp": "FUS",
+        "n_targets": 16,
+        "n_sig_terms": 0,
+        "has_sig": false,
+        "top_terms": []
+      },
+      {
+        "rbp": "FXR2",
+        "n_targets": 19,
+        "n_sig_terms": 13,
+        "has_sig": true,
+        "top_terms": [
+          "Synapse Organization (GO:0050808)",
+          "Protein Localization To Plasma Membrane (GO:0072659)",
+          "Protein Localization To Cell Periphery (GO:1990778)",
+          "Protein Localization To Membrane (GO:0072657)",
+          "Transcription By RNA Polymerase II (GO:0006366)"
+        ]
+      },
+      {
+        "rbp": "G3BP1",
+        "n_targets": 10,
+        "n_sig_terms": 0,
+        "has_sig": false,
+        "top_terms": []
+      },
+      {
+        "rbp": "HNRNPA1",
+        "n_targets": 102,
+        "n_sig_terms": 23,
+        "has_sig": true,
+        "top_terms": [
+          "Protein Modification Process (GO:0036211)",
+          "Protein Dephosphorylation (GO:0006470)",
+          "Purine-Containing Compound Metabolic Process (GO:0072521)",
+          "Dephosphorylation (GO:0016311)",
+          "Odontogenesis (GO:0042476)"
+        ]
+      },
+      {
+        "rbp": "HNRNPC",
+        "n_targets": 19,
+        "n_sig_terms": 6,
+        "has_sig": true,
+        "top_terms": [
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)",
+          "Cellular Response To Oxidative Stress (GO:0034599)",
+          "Protein Dephosphorylation (GO:0006470)",
+          "Dephosphorylation (GO:0016311)",
+          "Negative Regulation Of Cell Migration (GO:0030336)"
+        ]
+      },
+      {
+        "rbp": "HNRNPD",
+        "n_targets": 27,
+        "n_sig_terms": 5,
+        "has_sig": true,
+        "top_terms": [
+          "Response To Sterol (GO:0036314)",
+          "Odontogenesis (GO:0042476)",
+          "Regulation Of Smoothened Signaling Pathway (GO:0008589)",
+          "Regulation Of Lipid Metabolic Process (GO:0019216)",
+          "Regulation Of DNA-templated Transcription (GO:0006355)"
+        ]
+      },
+      {
+        "rbp": "HNRNPF",
+        "n_targets": 77,
+        "n_sig_terms": 10,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Response To Sterol (GO:0036314)",
+          "Epithelial Cell Morphogenesis (GO:0003382)",
+          "Nucleotide Metabolic Process (GO:0009117)",
+          "Regulation Of Adenylate Cyclase Activity (GO:0045761)"
+        ]
+      },
+      {
+        "rbp": "HNRNPK",
+        "n_targets": 40,
+        "n_sig_terms": 32,
+        "has_sig": true,
+        "top_terms": [
+          "Response To Sterol (GO:0036314)",
+          "Protein Modification Process (GO:0036211)",
+          "Positive Regulation Of TORC1 Signaling (GO:1904263)",
+          "Negative Regulation Of Proteasomal Ubiquitin-Dependent Protein Catabolic Process (GO:0032435)",
+          "Organonitrogen Compound Biosynthetic Process (GO:1901566)"
+        ]
+      },
+      {
+        "rbp": "HNRNPM",
+        "n_targets": 79,
+        "n_sig_terms": 32,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Response To Sterol (GO:0036314)",
+          "Epithelial Cell Morphogenesis (GO:0003382)",
+          "Regulation Of Intracellular Signal Transduction (GO:1902531)",
+          "Regulation Of DNA-templated Transcription (GO:0006355)"
+        ]
+      },
+      {
+        "rbp": "KHDRBS3",
+        "n_targets": 14,
+        "n_sig_terms": 4,
+        "has_sig": true,
+        "top_terms": [
+          "Insulin Secretion (GO:0030073)",
+          "Neurotransmitter Secretion (GO:0007269)",
+          "Synapse Organization (GO:0050808)",
+          "Chemical Synaptic Transmission (GO:0007268)"
+        ]
+      },
+      {
+        "rbp": "LARP7",
+        "n_targets": 10,
+        "n_sig_terms": 0,
+        "has_sig": false,
+        "top_terms": []
+      },
+      {
+        "rbp": "MBNL2",
+        "n_targets": 40,
+        "n_sig_terms": 13,
+        "has_sig": true,
+        "top_terms": [
+          "Protein Dephosphorylation (GO:0006470)",
+          "G2/M Transition Of Mitotic Cell Cycle (GO:0000086)",
+          "Cell Cycle G2/M Phase Transition (GO:0044839)",
+          "Dephosphorylation (GO:0016311)",
+          "Brain Development (GO:0007420)"
+        ]
+      },
+      {
+        "rbp": "NCL",
+        "n_targets": 56,
+        "n_sig_terms": 16,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Epithelial Cell Morphogenesis (GO:0003382)",
+          "Nucleotide Metabolic Process (GO:0009117)",
+          "Synapse Assembly (GO:0007416)",
+          "Epithelial Cell Development (GO:0002064)"
+        ]
+      },
+      {
+        "rbp": "NONO",
+        "n_targets": 74,
+        "n_sig_terms": 11,
+        "has_sig": true,
+        "top_terms": [
+          "Odontogenesis (GO:0042476)",
+          "Response To Sterol (GO:0036314)",
+          "Contractile Actin Filament Bundle Assembly (GO:0030038)",
+          "Odontogenesis Of Dentin-Containing Tooth (GO:0042475)",
+          "Stress Fiber Assembly (GO:0043149)"
+        ]
+      },
+      {
+        "rbp": "NPM1",
+        "n_targets": 140,
+        "n_sig_terms": 66,
+        "has_sig": true,
+        "top_terms": [
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)",
+          "Calcium Ion Import Across Plasma Membrane (GO:0098703)",
+          "Calcium Ion Transmembrane Transport (GO:0070588)",
+          "Calcium Ion Transport Into Cytosol (GO:0060402)",
+          "Cardiac Muscle Cell Action Potential (GO:0086001)"
+        ]
+      },
+      {
+        "rbp": "NUDT21",
+        "n_targets": 60,
+        "n_sig_terms": 6,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Response To Sterol (GO:0036314)",
+          "Epithelial Cell Morphogenesis (GO:0003382)",
+          "Epithelial Cell Development (GO:0002064)",
+          "Cell Morphogenesis Involved In Differentiation (GO:0000904)"
+        ]
+      },
+      {
+        "rbp": "PABPC1",
+        "n_targets": 72,
+        "n_sig_terms": 45,
+        "has_sig": true,
+        "top_terms": [
+          "Negative Regulation Of Cell Migration (GO:0030336)",
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)",
+          "Calcium Ion Transport Into Cytosol (GO:0060402)",
+          "Response To Sterol (GO:0036314)",
+          "Epithelial Cell Morphogenesis (GO:0003382)"
+        ]
+      },
+      {
+        "rbp": "PRKRA",
+        "n_targets": 10,
+        "n_sig_terms": 2,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Intracellular Signal Transduction (GO:1902531)",
+          "Regulation Of Cell Cycle (GO:0051726)"
+        ]
+      },
+      {
+        "rbp": "PTBP1",
+        "n_targets": 12,
+        "n_sig_terms": 2,
+        "has_sig": true,
+        "top_terms": [
+          "Organic Hydroxy Compound Biosynthetic Process (GO:1901617)",
+          "Steroid Biosynthetic Process (GO:0006694)"
+        ]
+      },
+      {
+        "rbp": "PTBP3",
+        "n_targets": 94,
+        "n_sig_terms": 21,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Regulation Of Cardiac Muscle Cell Membrane Repolarization (GO:0099623)",
+          "Establishment Of Centrosome Localization (GO:0051660)",
+          "Regulation Of Calcium Ion Transmembrane Transport Via High Voltage-Gated Calcium Channel (GO:1902514)",
+          "Negative Regulation Of Cell Migration (GO:0030336)"
+        ]
+      },
+      {
+        "rbp": "RBFOX2",
+        "n_targets": 13,
+        "n_sig_terms": 15,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Calcium Ion Transmembrane Transport Via High Voltage-Gated Calcium Channel (GO:1902514)",
+          "Positive Regulation Of Voltage-Gated Calcium Channel Activity (GO:1901387)",
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)",
+          "Regulation Of Heart Rate By Cardiac Conduction (GO:0086091)",
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)"
+        ]
+      },
+      {
+        "rbp": "RBFOX3",
+        "n_targets": 47,
+        "n_sig_terms": 29,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Calcium Ion Transmembrane Transport Via High Voltage-Gated Calcium Channel (GO:1902514)",
+          "Positive Regulation Of Voltage-Gated Calcium Channel Activity (GO:1901387)",
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)",
+          "Regulation Of Secretion (GO:0051046)",
+          "Calcium Ion Transmembrane Import Into Cytosol (GO:0097553)"
+        ]
+      },
+      {
+        "rbp": "SF3B1",
+        "n_targets": 43,
+        "n_sig_terms": 36,
+        "has_sig": true,
+        "top_terms": [
+          "Response To Sterol (GO:0036314)",
+          "Regulation Of Exocytosis (GO:0017157)",
+          "Positive Regulation Of Neurogenesis (GO:0050769)",
+          "Cytoskeleton Organization (GO:0007010)",
+          "Regulation Of Cell Morphogenesis (GO:0022604)"
+        ]
+      },
+      {
+        "rbp": "SFPQ",
+        "n_targets": 18,
+        "n_sig_terms": 2,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Nervous System Development (GO:0051962)",
+          "Positive Regulation Of Neurogenesis (GO:0050769)"
+        ]
+      },
+      {
+        "rbp": "SRSF1",
+        "n_targets": 33,
+        "n_sig_terms": 16,
+        "has_sig": true,
+        "top_terms": [
+          "Response To Sterol (GO:0036314)",
+          "Regulation Of DNA-templated Transcription (GO:0006355)",
+          "Negative Regulation Of Proteasomal Ubiquitin-Dependent Protein Catabolic Process (GO:0032435)",
+          "Negative Regulation Of Proteasomal Protein Catabolic Process (GO:1901799)",
+          "Negative Regulation Of Ubiquitin-Dependent Protein Catabolic Process (GO:2000059)"
+        ]
+      },
+      {
+        "rbp": "SRSF11",
+        "n_targets": 21,
+        "n_sig_terms": 5,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Lipid Metabolic Process (GO:0019216)",
+          "Regulation Of Anatomical Structure Morphogenesis (GO:0022603)",
+          "Adenylate Cyclase-Modulating G Protein-Coupled Receptor Signaling Pathway (GO:0007188)",
+          "Metal Ion Transport (GO:0030001)",
+          "Positive Regulation Of Transcription By RNA Polymerase II (GO:0045944)"
+        ]
+      },
+      {
+        "rbp": "SRSF2",
+        "n_targets": 43,
+        "n_sig_terms": 16,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Epithelial Cell Morphogenesis (GO:0003382)",
+          "Epithelial Cell Development (GO:0002064)",
+          "Cell Morphogenesis Involved In Differentiation (GO:0000904)",
+          "Negative Regulation Of Proteasomal Ubiquitin-Dependent Protein Catabolic Process (GO:0032435)"
+        ]
+      },
+      {
+        "rbp": "SRSF3",
+        "n_targets": 70,
+        "n_sig_terms": 4,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Calcium Ion Transmembrane Transport Via High Voltage-Gated Calcium Channel (GO:1902514)",
+          "Response To Sterol (GO:0036314)",
+          "Positive Regulation Of Voltage-Gated Calcium Channel Activity (GO:1901387)",
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)"
+        ]
+      },
+      {
+        "rbp": "SRSF7",
+        "n_targets": 29,
+        "n_sig_terms": 13,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Cell Projection Organization (GO:0031346)",
+          "Heterophilic Cell-Cell Adhesion Via Plasma Membrane Cell Adhesion Molecules (GO:0007157)",
+          "Positive Regulation Of Developmental Growth (GO:0048639)",
+          "Regulation Of Exocytosis (GO:0017157)",
+          "Positive Regulation Of Mitotic Cell Cycle Phase Transition (GO:1901992)"
+        ]
+      },
+      {
+        "rbp": "TNRC6B",
+        "n_targets": 12,
+        "n_sig_terms": 14,
+        "has_sig": true,
+        "top_terms": [
+          "Insulin Secretion (GO:0030073)",
+          "Neurotransmitter Secretion (GO:0007269)",
+          "Positive Regulation Of Synaptic Transmission (GO:0050806)",
+          "Cellular Response To Transforming Growth Factor Beta Stimulus (GO:0071560)",
+          "Cellular Response To Oxidative Stress (GO:0034599)"
+        ]
+      },
+      {
+        "rbp": "U2AF1",
+        "n_targets": 22,
+        "n_sig_terms": 9,
+        "has_sig": true,
+        "top_terms": [
+          "Response To Sterol (GO:0036314)",
+          "Regulation Of Smoothened Signaling Pathway (GO:0008589)",
+          "Regulation Of Lipid Metabolic Process (GO:0019216)",
+          "Regulation Of Nucleic Acid-Templated Transcription (GO:1903506)",
+          "Adenylate Cyclase-Modulating G Protein-Coupled Receptor Signaling Pathway (GO:0007188)"
+        ]
+      },
+      {
+        "rbp": "XRN2",
+        "n_targets": 24,
+        "n_sig_terms": 2,
+        "has_sig": true,
+        "top_terms": [
+          "Transcription By RNA Polymerase II (GO:0006366)",
+          "Proteolysis Involved In Protein Catabolic Process (GO:0051603)"
+        ]
+      },
+      {
+        "rbp": "YBX1",
+        "n_targets": 30,
+        "n_sig_terms": 20,
+        "has_sig": true,
+        "top_terms": [
+          "Cellular Response To Amyloid-Beta (GO:1904646)",
+          "Calcium Ion Import Across Plasma Membrane (GO:0098703)",
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Response To Amyloid-Beta (GO:1904645)",
+          "Heterophilic Cell-Cell Adhesion Via Plasma Membrane Cell Adhesion Molecules (GO:0007157)"
+        ]
+      },
+      {
+        "rbp": "YTHDF2",
+        "n_targets": 19,
+        "n_sig_terms": 2,
+        "has_sig": true,
+        "top_terms": [
+          "Proteolysis Involved In Protein Catabolic Process (GO:0051603)",
+          "Adenylate Cyclase-Modulating G Protein-Coupled Receptor Signaling Pathway (GO:0007188)"
+        ]
+      },
+      {
+        "rbp": "ZFP36L1",
+        "n_targets": 97,
+        "n_sig_terms": 54,
+        "has_sig": true,
+        "top_terms": [
+          "Membrane Depolarization During Cardiac Muscle Cell Action Potential (GO:0086012)",
+          "Calcium Ion Import Across Plasma Membrane (GO:0098703)",
+          "Regulation Of Heart Rate By Cardiac Conduction (GO:0086091)",
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Cardiac Conduction (GO:0061337)"
+        ]
+      }
+    ]
+  },
+  "dentate_gyrus": {
+    "n_eligible_rbps": 17,
+    "n_with_sig_go": 17,
+    "frac_with_sig_go": 1.0,
+    "mean_cross_rbp_jaccard": 0.173640289449113,
+    "n_known_biology_matches": 1,
+    "concordance_hits": [
+      {
+        "rbp": "RBFOX3",
+        "matched_keywords": [
+          "synap"
+        ]
+      }
+    ],
+    "bootstrap_null_frac": 0.916,
+    "per_rbp": [
+      {
+        "rbp": "CELF1",
+        "n_targets": 16,
+        "n_sig_terms": 13,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Regulation Of Dendritic Spine Morphogenesis (GO:0061001)",
+          "Regulation Of Neuron Projection Development (GO:0010975)"
+        ]
+      },
+      {
+        "rbp": "CELF4",
+        "n_targets": 31,
+        "n_sig_terms": 24,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of JNK Cascade (GO:0046328)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Regulation Of Dendritic Spine Morphogenesis (GO:0061001)"
+        ]
+      },
+      {
+        "rbp": "DDX39B",
+        "n_targets": 19,
+        "n_sig_terms": 21,
+        "has_sig": true,
+        "top_terms": [
+          "Regulation Of Ubiquitin-Dependent Protein Catabolic Process (GO:2000058)",
+          "Regulation Of Cell-Cell Adhesion (GO:0022407)",
+          "Positive Regulation Of Apoptotic Process (GO:0043065)",
+          "Protein Autoubiquitination (GO:0051865)",
+          "Positive Regulation Of JNK Cascade (GO:0046330)"
+        ]
+      },
+      {
+        "rbp": "ELAVL3",
+        "n_targets": 26,
+        "n_sig_terms": 18,
+        "has_sig": true,
+        "top_terms": [
+          "Cardiac Muscle Cell Development (GO:0055013)",
+          "RNA Biosynthetic Process (GO:0032774)",
+          "Negative Regulation Of Cell Motility (GO:2000146)",
+          "Positive Regulation Of RNA Splicing (GO:0033120)",
+          "Negative Regulation Of Cell Migration (GO:0030336)"
+        ]
+      },
+      {
+        "rbp": "ELAVL4",
+        "n_targets": 14,
+        "n_sig_terms": 3,
+        "has_sig": true,
+        "top_terms": [
+          "Monoatomic Cation Homeostasis (GO:0055080)",
+          "Positive Regulation Of Cell Projection Organization (GO:0031346)",
+          "Chemical Synaptic Transmission (GO:0007268)"
+        ]
+      },
+      {
+        "rbp": "HNRNPA1",
+        "n_targets": 55,
+        "n_sig_terms": 28,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Nervous System Development (GO:0007399)",
+          "Ephrin Receptor Signaling Pathway (GO:0048013)",
+          "Neuron Projection Guidance (GO:0097485)",
+          "Neuron Migration (GO:0001764)"
+        ]
+      },
+      {
+        "rbp": "HNRNPC",
+        "n_targets": 14,
+        "n_sig_terms": 27,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Cell-Substrate Junction Assembly (GO:0090109)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Regulation Of Dendritic Spine Morphogenesis (GO:0061001)"
+        ]
+      },
+      {
+        "rbp": "MBNL2",
+        "n_targets": 27,
+        "n_sig_terms": 21,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Positive Regulation Of Calcium Ion Transmembrane Transporter Activity (GO:1901021)",
+          "Regulation Of Dendritic Spine Morphogenesis (GO:0061001)"
+        ]
+      },
+      {
+        "rbp": "NONO",
+        "n_targets": 16,
+        "n_sig_terms": 19,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Regulation Of Dendritic Spine Morphogenesis (GO:0061001)",
+          "Vesicle Cytoskeletal Trafficking (GO:0099518)"
+        ]
+      },
+      {
+        "rbp": "NPM1",
+        "n_targets": 45,
+        "n_sig_terms": 25,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Nervous System Development (GO:0007399)",
+          "Regulation Of Neuron Projection Development (GO:0010975)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Cell Junction Assembly (GO:0034329)"
+        ]
+      },
+      {
+        "rbp": "NUDT21",
+        "n_targets": 36,
+        "n_sig_terms": 31,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Regulation Of JNK Cascade (GO:0046328)",
+          "Regulation Of Protein Transport (GO:0051223)"
+        ]
+      },
+      {
+        "rbp": "PABPC1",
+        "n_targets": 26,
+        "n_sig_terms": 10,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Calcium Ion Transmembrane Transporter Activity (GO:1901021)",
+          "Cell Cycle G2/M Phase Transition (GO:0044839)",
+          "Cellular Response To Oxygen-Containing Compound (GO:1901701)",
+          "Positive Regulation Of Apoptotic Process (GO:0043065)",
+          "Calcium-Mediated Signaling (GO:0019722)"
+        ]
+      },
+      {
+        "rbp": "RBFOX1",
+        "n_targets": 25,
+        "n_sig_terms": 12,
+        "has_sig": true,
+        "top_terms": [
+          "Protein Autoubiquitination (GO:0051865)",
+          "Positive Regulation Of JNK Cascade (GO:0046330)",
+          "Positive Regulation Of Protein Modification By Small Protein Conjugation Or Removal (GO:1903322)",
+          "Positive Regulation Of Apoptotic Process (GO:0043065)",
+          "Positive Regulation Of Protein Ubiquitination (GO:0031398)"
+        ]
+      },
+      {
+        "rbp": "RBFOX2",
+        "n_targets": 15,
+        "n_sig_terms": 6,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Apoptotic Process (GO:0043065)",
+          "Protein Autophosphorylation (GO:0046777)",
+          "Phosphate-Containing Compound Metabolic Process (GO:0006796)",
+          "Positive Regulation Of Programmed Cell Death (GO:0043068)",
+          "Regulation Of Apoptotic Process (GO:0042981)"
+        ]
+      },
+      {
+        "rbp": "RBFOX3",
+        "n_targets": 12,
+        "n_sig_terms": 11,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)",
+          "Regulation Of Dendritic Spine Morphogenesis (GO:0061001)",
+          "Vesicle Cytoskeletal Trafficking (GO:0099518)"
+        ]
+      },
+      {
+        "rbp": "SRSF7",
+        "n_targets": 30,
+        "n_sig_terms": 30,
+        "has_sig": true,
+        "top_terms": [
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)",
+          "Response To Muscle Stretch (GO:0035994)",
+          "Regulation Of Cell-Substrate Junction Assembly (GO:0090109)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Regulation Of Postsynapse Organization (GO:0099175)"
+        ]
+      },
+      {
+        "rbp": "YBX1",
+        "n_targets": 97,
+        "n_sig_terms": 67,
+        "has_sig": true,
+        "top_terms": [
+          "Chemical Synaptic Transmission (GO:0007268)",
+          "Modulation Of Chemical Synaptic Transmission (GO:0050804)",
+          "Nervous System Development (GO:0007399)",
+          "Regulation Of Dendritic Spine Development (GO:0060998)",
+          "Dense Core Granule Cytoskeletal Transport (GO:0099519)"
+        ]
+      }
+    ]
+  },
+  "neuroblastoma": {
+    "n_eligible_rbps": 12,
+    "n_with_sig_go": 12,
+    "frac_with_sig_go": 1.0,
+    "mean_cross_rbp_jaccard": 0.09926647426647427,
+    "n_known_biology_matches": 0,
+    "concordance_hits": [],
+    "bootstrap_null_frac": 0.9119999999999999,
+    "per_rbp": [
+      {
+        "rbp": "FUS",
+        "n_targets": 14,
+        "n_sig_terms": 3,
+        "has_sig": true,
+        "top_terms": [
+          "Actomyosin Structure Organization (GO:0031032)",
+          "Phosphate-Containing Compound Metabolic Process (GO:0006796)",
+          "Positive Regulation Of Signal Transduction (GO:0009967)"
+        ]
+      },
+      {
+        "rbp": "HNRNPA2B1",
+        "n_targets": 46,
+        "n_sig_terms": 29,
+        "has_sig": true,
+        "top_terms": [
+          "Negative Regulation Of Fat Cell Differentiation (GO:0045599)",
+          "Positive Regulation Of Vascular Endothelial Growth Factor Signaling Pathway (GO:1900748)",
+          "Regulation Of Fat Cell Differentiation (GO:0045598)",
+          "Regulation Of Vascular Endothelial Growth Factor Signaling Pathway (GO:1900746)",
+          "Positive Regulation Of Neuron Projection Development (GO:0010976)"
+        ]
+      },
+      {
+        "rbp": "HNRNPD",
+        "n_targets": 18,
+        "n_sig_terms": 11,
+        "has_sig": true,
+        "top_terms": [
+          "Axonogenesis (GO:0007409)",
+          "Positive Regulation Of Cell Migration (GO:0030335)",
+          "Positive Regulation Of Epithelial Cell Migration (GO:0010634)",
+          "Neuron Projection Guidance (GO:0097485)",
+          "Axon Guidance (GO:0007411)"
+        ]
+      },
+      {
+        "rbp": "HNRNPK",
+        "n_targets": 14,
+        "n_sig_terms": 6,
+        "has_sig": true,
+        "top_terms": [
+          "Neuron Development (GO:0048666)",
+          "Neuron Differentiation (GO:0030182)",
+          "Phosphate-Containing Compound Metabolic Process (GO:0006796)",
+          "Positive Regulation Of Signal Transduction (GO:0009967)",
+          "Nervous System Development (GO:0007399)"
+        ]
+      },
+      {
+        "rbp": "HNRNPU",
+        "n_targets": 18,
+        "n_sig_terms": 13,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of DNA-binding Transcription Factor Activity (GO:0051091)",
+          "Positive Regulation Of NF-kappaB Transcription Factor Activity (GO:0051092)",
+          "Regulation Of Dendrite Development (GO:0050773)",
+          "Protein Phosphorylation (GO:0006468)",
+          "Muscle Organ Development (GO:0007517)"
+        ]
+      },
+      {
+        "rbp": "NCL",
+        "n_targets": 12,
+        "n_sig_terms": 6,
+        "has_sig": true,
+        "top_terms": [
+          "Neuron Development (GO:0048666)",
+          "Positive Regulation Of NF-kappaB Transcription Factor Activity (GO:0051092)",
+          "Phosphate-Containing Compound Metabolic Process (GO:0006796)",
+          "Positive Regulation Of DNA-binding Transcription Factor Activity (GO:0051091)",
+          "Regulation Of Gene Expression (GO:0010468)"
+        ]
+      },
+      {
+        "rbp": "PABPC1",
+        "n_targets": 28,
+        "n_sig_terms": 24,
+        "has_sig": true,
+        "top_terms": [
+          "Axonogenesis (GO:0007409)",
+          "Protein Phosphorylation (GO:0006468)",
+          "Positive Regulation Of Small Molecule Metabolic Process (GO:0062013)",
+          "Positive Regulation Of Carbohydrate Metabolic Process (GO:0045913)",
+          "Ephrin Receptor Signaling Pathway (GO:0048013)"
+        ]
+      },
+      {
+        "rbp": "PRPF8",
+        "n_targets": 17,
+        "n_sig_terms": 9,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Neuron Projection Development (GO:0010976)",
+          "Actomyosin Structure Organization (GO:0031032)",
+          "Positive Regulation Of DNA Metabolic Process (GO:0051054)",
+          "Positive Regulation Of Cell Projection Organization (GO:0031346)",
+          "Actin Filament Organization (GO:0007015)"
+        ]
+      },
+      {
+        "rbp": "SNRNP200",
+        "n_targets": 16,
+        "n_sig_terms": 12,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Signal Transduction (GO:0009967)",
+          "Macroautophagy (GO:0016236)",
+          "Phosphorylation (GO:0016310)",
+          "Positive Regulation Of NF-kappaB Transcription Factor Activity (GO:0051092)",
+          "Protein Phosphorylation (GO:0006468)"
+        ]
+      },
+      {
+        "rbp": "SRSF3",
+        "n_targets": 11,
+        "n_sig_terms": 6,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Epithelial Cell Migration (GO:0010634)",
+          "Phosphate-Containing Compound Metabolic Process (GO:0006796)",
+          "Positive Regulation Of Signal Transduction (GO:0009967)",
+          "Positive Regulation Of Cell Migration (GO:0030335)",
+          "Phosphorylation (GO:0016310)"
+        ]
+      },
+      {
+        "rbp": "SRSF7",
+        "n_targets": 10,
+        "n_sig_terms": 4,
+        "has_sig": true,
+        "top_terms": [
+          "Positive Regulation Of Epithelial Cell Migration (GO:0010634)",
+          "Phosphate-Containing Compound Metabolic Process (GO:0006796)",
+          "Phosphorylation (GO:0016310)",
+          "Protein Phosphorylation (GO:0006468)"
+        ]
+      },
+      {
+        "rbp": "YBX1",
+        "n_targets": 21,
+        "n_sig_terms": 15,
+        "has_sig": true,
+        "top_terms": [
+          "Neuron Development (GO:0048666)",
+          "Positive Regulation Of DNA-binding Transcription Factor Activity (GO:0051091)",
+          "Positive Regulation Of Signal Transduction (GO:0009967)",
+          "Positive Regulation Of Neuron Projection Development (GO:0010976)",
+          "Phosphorylation (GO:0016310)"
+        ]
+      }
+    ]
+  }
+}

output/comprehensive_improvements/results/nb_split_half.json

@@ -0,0 +1,157 @@
+{
+  "full_data_n_edges": 326,
+  "full_data_top_hubs": [
+    "HNRNPA2B1",
+    "PABPC1",
+    "YBX1",
+    "HNRNPD",
+    "HNRNPU",
+    "PRPF8",
+    "SNRNP200",
+    "FUS",
+    "HNRNPK",
+    "NCL",
+    "SRSF3",
+    "SRSF7",
+    "EWSR1",
+    "SNRPA",
+    "PTBP1",
+    "TRA2B",
+    "QKI",
+    "HNRNPM",
+    "SRSF10",
+    "DDX5"
+  ],
+  "n_replicates": 5,
+  "mean_jaccard": 0.6133333333333334,
+  "std_jaccard": 0.026666666666666665,
+  "mean_hub_count_r": 0.8265151271154416,
+  "replicates": [
+    {
+      "replicate": 1,
+      "jaccard_half_half": 0.6666666666666666,
+      "hub_count_spearman_r": 0.9468522589014116,
+      "jaccard_half1_full": 0.6666666666666666,
+      "jaccard_half2_full": 0.6,
+      "n_shared_rbps": 23,
+      "overlap_hubs": [
+        "CPEB3",
+        "DDX5",
+        "FUS",
+        "HNRNPA2B1",
+        "HNRNPD",
+        "HNRNPK",
+        "HNRNPM",
+        "HNRNPU",
+        "PABPC1",
+        "PRPF8",
+        "RBFOX2",
+        "SNRNP200",
+        "SNRPA",
+        "SRSF3",
+        "SRSF7",
+        "YBX1"
+      ]
+    },
+    {
+      "replicate": 2,
+      "jaccard_half_half": 0.6,
+      "hub_count_spearman_r": 0.6604959343878761,
+      "jaccard_half1_full": 0.6,
+      "jaccard_half2_full": 0.48148148148148145,
+      "n_shared_rbps": 25,
+      "overlap_hubs": [
+        "CPEB3",
+        "DDX17",
+        "EWSR1",
+        "FUS",
+        "HNRNPA2B1",
+        "HNRNPD",
+        "HNRNPK",
+        "HNRNPM",
+        "HNRNPU",
+        "NCL",
+        "PABPC1",
+        "PRPF8",
+        "SRSF3",
+        "SRSF7",
+        "YBX1"
+      ]
+    },
+    {
+      "replicate": 3,
+      "jaccard_half_half": 0.6,
+      "hub_count_spearman_r": 0.8850422405862888,
+      "jaccard_half1_full": 0.6,
+      "jaccard_half2_full": 0.6,
+      "n_shared_rbps": 20,
+      "overlap_hubs": [
+        "CPEB3",
+        "DDX17",
+        "DDX5",
+        "FUS",
+        "HNRNPA2B1",
+        "HNRNPD",
+        "HNRNPK",
+        "HNRNPU",
+        "NCL",
+        "PABPC1",
+        "PRPF8",
+        "SNRNP200",
+        "SRSF3",
+        "SRSF7",
+        "YBX1"
+      ]
+    },
+    {
+      "replicate": 4,
+      "jaccard_half_half": 0.6,
+      "hub_count_spearman_r": 0.8395104191517644,
+      "jaccard_half1_full": 0.5384615384615384,
+      "jaccard_half2_full": 0.6,
+      "n_shared_rbps": 21,
+      "overlap_hubs": [
+        "CPEB3",
+        "DDX5",
+        "FUS",
+        "HNRNPA2B1",
+        "HNRNPC",
+        "HNRNPD",
+        "HNRNPK",
+        "HNRNPM",
+        "HNRNPU",
+        "PABPC1",
+        "PRPF8",
+        "SNRNP200",
+        "SRSF3",
+        "SRSF7",
+        "YBX1"
+      ]
+    },
+    {
+      "replicate": 5,
+      "jaccard_half_half": 0.6,
+      "hub_count_spearman_r": 0.8006747825498669,
+      "jaccard_half1_full": 0.6,
+      "jaccard_half2_full": 0.6,
+      "n_shared_rbps": 25,
+      "overlap_hubs": [
+        "CPEB3",
+        "DDX17",
+        "DDX5",
+        "FUS",
+        "HNRNPA2B1",
+        "HNRNPD",
+        "HNRNPK",
+        "HNRNPM",
+        "HNRNPU",
+        "PABPC1",
+        "PRPF8",
+        "SNRNP200",
+        "SRSF3",
+        "SRSF7",
+        "YBX1"
+      ]
+    }
+  ]
+}

output/comprehensive_improvements/results/pathway_consistency.json

@@ -0,0 +1,32 @@
+[
+  {
+    "pair": "dentate_gyrus vs pancreas",
+    "gene_level_r": 0.1915326245338796,
+    "gene_level_p": 7.922783245030365e-42,
+    "n_shared_genes": 4915,
+    "pathway_level_r": 0.3250710810771724,
+    "pathway_level_p": 1.6099238674694722e-32,
+    "n_pathways": 1265,
+    "mean_pathway_size": 27.791304347826088
+  },
+  {
+    "pair": "dentate_gyrus vs scifate",
+    "gene_level_r": 0.08447339384620146,
+    "gene_level_p": 8.67540553346651e-07,
+    "n_shared_genes": 3382,
+    "pathway_level_r": 0.21288020530561333,
+    "pathway_level_p": 1.961375216882019e-11,
+    "n_pathways": 973,
+    "mean_pathway_size": 26.696813977389517
+  },
+  {
+    "pair": "pancreas vs scifate",
+    "gene_level_r": 0.27801667286917026,
+    "gene_level_p": 1.0536113634681191e-114,
+    "n_shared_genes": 6444,
+    "pathway_level_r": 0.2756626839019158,
+    "pathway_level_p": 1.1058800617873004e-32,
+    "n_pathways": 1796,
+    "mean_pathway_size": 32.2271714922049
+  }
+]

output/deep_benchmarks/01_fair_comparison/results/dentate_gyrus_fair_comparison.json

@@ -0,0 +1,30 @@
+{
+  "mouse": {
+    "analytical_all": {
+      "r": -0.3179587682344816,
+      "n": 1217
+    },
+    "analytical_300": {
+      "r": -0.28646904360419734,
+      "n": 203
+    },
+    "deepptr_300": {
+      "r": -0.2852053996865196,
+      "n": 216
+    }
+  },
+  "human": {
+    "analytical_all": {
+      "r": -0.3812073018847205,
+      "n": 1126
+    },
+    "analytical_300": {
+      "r": -0.3593371092867718,
+      "n": 199
+    },
+    "deepptr_300": {
+      "r": -0.35768791768630437,
+      "n": 211
+    }
+  }
+}

output/deep_benchmarks/01_fair_comparison/results/pancreas_fair_comparison.json

@@ -0,0 +1,30 @@
+{
+  "mouse": {
+    "analytical_all": {
+      "r": -0.34966929477006137,
+      "n": 4611
+    },
+    "analytical_300": {
+      "r": -0.2040166725324759,
+      "n": 236
+    },
+    "deepptr_300": {
+      "r": -0.19762101977653473,
+      "n": 251
+    }
+  },
+  "human": {
+    "analytical_all": {
+      "r": -0.4020872107350974,
+      "n": 4308
+    },
+    "analytical_300": {
+      "r": -0.22231279755152644,
+      "n": 219
+    },
+    "deepptr_300": {
+      "r": -0.2767452667406712,
+      "n": 236
+    }
+  }
+}

output/deep_benchmarks/02_bootstrap_ci/results/bootstrap_ci.json

@@ -0,0 +1,34 @@
+{
+  "pancreas": {
+    "mouse": {
+      "r": -0.34966929477006137,
+      "ci_lo": -0.37505541284510563,
+      "ci_hi": -0.32339213617024476,
+      "se": 0.01339371294186963,
+      "n": 4611
+    },
+    "human": {
+      "r": -0.4020872107350974,
+      "ci_lo": -0.4276468985736799,
+      "ci_hi": -0.3764103388779307,
+      "se": 0.013602976735564256,
+      "n": 4308
+    }
+  },
+  "dentate_gyrus": {
+    "mouse": {
+      "r": -0.3179587682344816,
+      "ci_lo": -0.3698980291843292,
+      "ci_hi": -0.2659465445853813,
+      "se": 0.02700541514025033,
+      "n": 1217
+    },
+    "human": {
+      "r": -0.3812073018847205,
+      "ci_lo": -0.4298039591317201,
+      "ci_hi": -0.32596791229798067,
+      "se": 0.026761058702956173,
+      "n": 1126
+    }
+  }
+}

output/deep_benchmarks/03_eclip_validation/results/eclip_validation.json

@@ -0,0 +1,169 @@
+{
+  "pancreas": {
+    "n_pt_genes": 44,
+    "n_in_eclip": 23,
+    "frac_in_eclip": 0.5227272727272727,
+    "fisher_odds": 1.6595783351508542,
+    "fisher_p": 0.063168839215465,
+    "validated_genes": [
+      "ADGRB3",
+      "CHCHD3",
+      "DIP2C",
+      "DNAJC1",
+      "EGLN2",
+      "FARP1",
+      "FBXL17",
+      "FHIT",
+      "IGF2BP2",
+      "KCNQ1",
+      "MBD5",
+      "NR6A1",
+      "PAN3",
+      "PHLDB2",
+      "PTPRN2",
+      "RORA",
+      "SDK1",
+      "SND1",
+      "TCF12",
+      "TMCC1",
+      "TTLL3",
+      "WWOX",
+      "ZMYND8"
+    ],
+    "top_rbps": {
+      "MATR3": [
+        "ADGRB3",
+        "CHCHD3",
+        "FARP1",
+        "FBXL17",
+        "FHIT",
+        "IGF2BP2",
+        "KCNQ1",
+        "MBD5",
+        "NR6A1",
+        "PAN3",
+        "PHLDB2",
+        "PTPRN2",
+        "SDK1",
+        "SND1",
+        "TCF12",
+        "WWOX",
+        "ZMYND8"
+      ],
+      "ELAVL1": [
+        "ADGRB3",
+        "CHCHD3",
+        "DNAJC1",
+        "FARP1",
+        "FHIT",
+        "IGF2BP2",
+        "MBD5",
+        "NR6A1",
+        "PAN3",
+        "SDK1",
+        "SND1",
+        "TCF12",
+        "TMCC1",
+        "ZMYND8"
+      ],
+      "RBFOX2": [
+        "DIP2C",
+        "FARP1",
+        "FHIT",
+        "IGF2BP2",
+        "KCNQ1",
+        "NR6A1",
+        "PTPRN2",
+        "SND1",
+        "TCF12",
+        "TTLL3",
+        "WWOX",
+        "ZMYND8"
+      ],
+      "FUS": [
+        "DIP2C",
+        "EGLN2",
+        "FARP1",
+        "KCNQ1",
+        "PTPRN2",
+        "RORA",
+        "SND1",
+        "TTLL3",
+        "ZMYND8"
+      ],
+      "HNRNPC": [
+        "FARP1",
+        "IGF2BP2",
+        "MBD5",
+        "PAN3",
+        "PTPRN2",
+        "SND1",
+        "TCF12",
+        "WWOX",
+        "ZMYND8"
+      ],
+      "HNRNPU": [
+        "FARP1",
+        "KCNQ1",
+        "SND1",
+        "ZMYND8"
+      ],
+      "MBNL2": [
+        "KCNQ1",
+        "MBD5",
+        "TCF12",
+        "ZMYND8"
+      ],
+      "TRA2B": [
+        "KCNQ1",
+        "TTLL3",
+        "ZMYND8"
+      ],
+      "HNRNPA1": [
+        "KCNQ1"
+      ]
+    },
+    "are_overlap": [],
+    "nmd_overlap": []
+  },
+  "dentate_gyrus": {
+    "n_pt_genes": 11,
+    "n_in_eclip": 5,
+    "frac_in_eclip": 0.45454545454545453,
+    "fisher_odds": 1.0486612834679132,
+    "fisher_p": 0.5840022381352574,
+    "validated_genes": [
+      "CDH8",
+      "CNOT6",
+      "EML6",
+      "SCFD1",
+      "TAF13"
+    ],
+    "top_rbps": {
+      "MATR3": [
+        "CNOT6",
+        "EML6",
+        "SCFD1"
+      ],
+      "ELAVL1": [
+        "CNOT6",
+        "SCFD1"
+      ],
+      "HNRNPC": [
+        "CNOT6",
+        "SCFD1"
+      ],
+      "HNRNPA1": [
+        "CDH8"
+      ],
+      "RBFOX2": [
+        "EML6"
+      ],
+      "TRA2B": [
+        "TAF13"
+      ]
+    },
+    "are_overlap": [],
+    "nmd_overlap": []
+  }
+}

output/deep_benchmarks/04_scifate_tautology/results/scifate_tautology.json

@@ -0,0 +1,9 @@
+{
+  "r_gamma_gt": 0.992817592890788,
+  "r_residual": 0.9984800928036497,
+  "r_raw": 0.9649445360200416,
+  "beta_cv": 1.3545215701232527,
+  "pipeline_delta_r": 0.02787305687074637,
+  "severity": "high",
+  "n_genes": 7927
+}

output/deep_benchmarks/05_sparsity/results/dentate_gyrus_sparsity.json

@@ -0,0 +1,29 @@
+{
+  "dataset": "dentate_gyrus",
+  "stratified": [
+    {
+      "quartile": "Q1 (sparse)",
+      "n": 284,
+      "r": -0.43071286525006675,
+      "med_det": 0.03447098976109215
+    },
+    {
+      "quartile": "Q2",
+      "n": 282,
+      "r": -0.337181680598891,
+      "med_det": 0.05
+    },
+    {
+      "quartile": "Q3",
+      "n": 279,
+      "r": -0.30982074466292286,
+      "med_det": 0.08156996587030717
+    },
+    {
+      "quartile": "Q4 (dense)",
+      "n": 281,
+      "r": -0.389195011247454,
+      "med_det": 0.18976109215017065
+    }
+  ]
+}

output/deep_benchmarks/05_sparsity/results/pancreas_sparsity.json

@@ -0,0 +1,29 @@
+{
+  "dataset": "pancreas",
+  "stratified": [
+    {
+      "quartile": "Q1 (sparse)",
+      "n": 1081,
+      "r": -0.4687958859652454,
+      "med_det": 0.036255411255411256
+    },
+    {
+      "quartile": "Q2",
+      "n": 1075,
+      "r": -0.41976278876881845,
+      "med_det": 0.06818181818181818
+    },
+    {
+      "quartile": "Q3",
+      "n": 1079,
+      "r": -0.33749931613006473,
+      "med_det": 0.12094155844155845
+    },
+    {
+      "quartile": "Q4 (dense)",
+      "n": 1073,
+      "r": -0.29304334559984213,
+      "med_det": 0.25405844155844154
+    }
+  ]
+}

output/deep_benchmarks/06_ci_coverage/results/ci_coverage.json

@@ -0,0 +1,28 @@
+{
+  "overall_coverage": 0.24504666666666666,
+  "ci_width": 0.2263760268688202,
+  "true_range": 3.041830062866211,
+  "rel_error": 0.36981287598609924,
+  "calibration": [
+    {
+      "nominal": 0.5,
+      "actual": 0.08518
+    },
+    {
+      "nominal": 0.8,
+      "actual": 0.16124
+    },
+    {
+      "nominal": 0.9,
+      "actual": 0.20678
+    },
+    {
+      "nominal": 0.95,
+      "actual": 0.24504666666666666
+    },
+    {
+      "nominal": 0.99,
+      "actual": 0.3164533333333333
+    }
+  ]
+}

output/deep_benchmarks/07_reconstruction/results/reconstruction.json

@@ -0,0 +1,132 @@
+{
+  "pancreas": {
+    "median_ll_per_gene": -1.7233030796051025,
+    "median_ll_baseline": -1.7099657365822716,
+    "n_improved": 104,
+    "n_genes": 300,
+    "final_train_loss": 578.9812098911831,
+    "final_val_loss": 581.9227905273438,
+    "per_celltype": [
+      {
+        "cell_type": "Alpha",
+        "n_cells": 481,
+        "mean_ll": -615.6022338867188
+      },
+      {
+        "cell_type": "Beta",
+        "n_cells": 591,
+        "mean_ll": -594.2098388671875
+      },
+      {
+        "cell_type": "Delta",
+        "n_cells": 70,
+        "mean_ll": -604.226318359375
+      },
+      {
+        "cell_type": "Ductal",
+        "n_cells": 916,
+        "mean_ll": -509.6988830566406
+      },
+      {
+        "cell_type": "Epsilon",
+        "n_cells": 142,
+        "mean_ll": -599.9423217773438
+      },
+      {
+        "cell_type": "Ngn3 high EP",
+        "n_cells": 642,
+        "mean_ll": -566.7362670898438
+      },
+      {
+        "cell_type": "Ngn3 low EP",
+        "n_cells": 262,
+        "mean_ll": -529.7142333984375
+      },
+      {
+        "cell_type": "Pre-endocrine",
+        "n_cells": 592,
+        "mean_ll": -624.0943603515625
+      }
+    ]
+  },
+  "dentate_gyrus": {
+    "median_ll_per_gene": -1.2623636722564697,
+    "median_ll_baseline": -1.0423157516088688,
+    "n_improved": 66,
+    "n_genes": 300,
+    "final_train_loss": 446.1490020751953,
+    "final_val_loss": 442.7923278808594,
+    "per_celltype": [
+      {
+        "cell_type": "Astrocytes",
+        "n_cells": 120,
+        "mean_ll": -320.6481628417969
+      },
+      {
+        "cell_type": "Cajal Retzius",
+        "n_cells": 34,
+        "mean_ll": -406.7076416015625
+      },
+      {
+        "cell_type": "Cck-Tox",
+        "n_cells": 27,
+        "mean_ll": -478.2455749511719
+      },
+      {
+        "cell_type": "Endothelial",
+        "n_cells": 87,
+        "mean_ll": -269.2615966796875
+      },
+      {
+        "cell_type": "GABA",
+        "n_cells": 61,
+        "mean_ll": -436.56988525390625
+      },
+      {
+        "cell_type": "Granule immature",
+        "n_cells": 785,
+        "mean_ll": -467.5433654785156
+      },
+      {
+        "cell_type": "Granule mature",
+        "n_cells": 1070,
+        "mean_ll": -487.29730224609375
+      },
+      {
+        "cell_type": "Microglia",
+        "n_cells": 81,
+        "mean_ll": -252.7560272216797
+      },
+      {
+        "cell_type": "Mossy",
+        "n_cells": 75,
+        "mean_ll": -468.4962463378906
+      },
+      {
+        "cell_type": "Neuroblast",
+        "n_cells": 417,
+        "mean_ll": -409.8547058105469
+      },
+      {
+        "cell_type": "OL",
+        "n_cells": 50,
+        "mean_ll": -311.520263671875
+      },
+      {
+        "cell_type": "OPC",
+        "n_cells": 53,
+        "mean_ll": -408.2958068847656
+      },
+      {
+        "cell_type": "Radial Glia-like",
+        "n_cells": 51,
+        "mean_ll": -316.1266784667969
+      },
+      {
+        "cell_type": "nIPC",
+        "n_cells": 19,
+        "mean_ll": -316.6011047363281
+      }
+    ]
+  }
+}

output/deep_benchmarks/08_temporal_latent/results/dentate_gyrus_temporal.json

@@ -0,0 +1,37 @@
+{
+  "pseudotime": {
+    "max_r_zT": 0.6376333811909575,
+    "max_r_zPT": 0.5588258384356067,
+    "r_zT_dims": [
+      -0.41192172021218787,
+      -0.18985164712855934,
+      0.42794390633870044,
+      -0.08310248704473128,
+      0.6376333811909575,
+      0.08213203229581705,
+      -0.05149820576222774,
+      0.2727290780641637
+    ],
+    "r_zPT_dims": [
+      -0.5588258384356067,
+      0.4938356446261747,
+      -0.21959396856034535,
+      -0.3963924861122928,
+      -0.2514719444971854,
+      0.2880478070440341,
+      -0.18460598096991557,
+      -0.3817162419543668
+    ]
+  },
+  "silhouette": {
+    "expression": 0.01724175177514553,
+    "z_T": 0.16729028522968292,
+    "z_PT": 0.05307881534099579,
+    "gamma": -0.08686356991529465
+  },
+  "variance_explained": {
+    "z_T": 0.9999999403953552,
+    "z_PT": 1.0
+  },
+  "final_kl": 4.9496833483378095
+}

output/deep_benchmarks/08_temporal_latent/results/pancreas_temporal.json

@@ -0,0 +1,37 @@
+{
+  "pseudotime": {
+    "max_r_zT": 0.8500275841367113,
+    "max_r_zPT": 0.755434322667789,
+    "r_zT_dims": [
+      0.010221207770288192,
+      -0.36421185343358486,
+      -0.19323067203801877,
+      -0.8500275841367113,
+      -0.15643935118680982,
+      0.5417209379611388,
+      0.3692436231875954,
+      0.3427429925453924
+    ],
+    "r_zPT_dims": [
+      0.16365064690613063,
+      0.48529397291021903,
+      -0.13147202332120686,
+      0.7235643406635327,
+      -0.46782528609669133,
+      -0.007959426548289739,
+      0.7005066849391194,
+      -0.755434322667789
+    ]
+  },
+  "silhouette": {
+    "expression": 0.0922398641705513,
+    "z_T": 0.21077203750610352,
+    "z_PT": 0.008416243828833103,
+    "gamma": -0.12521205842494965
+  },
+  "variance_explained": {
+    "z_T": 1.0,
+    "z_PT": 1.0
+  },
+  "final_kl": 6.077418736049107
+}

output/deep_benchmarks/08_temporal_latent/results/temporal_all.json

@@ -0,0 +1,76 @@
+{
+  "pancreas": {
+    "pseudotime": {
+      "max_r_zT": 0.8500275841367113,
+      "max_r_zPT": 0.755434322667789,
+      "r_zT_dims": [
+        0.010221207770288192,
+        -0.36421185343358486,
+        -0.19323067203801877,
+        -0.8500275841367113,
+        -0.15643935118680982,
+        0.5417209379611388,
+        0.3692436231875954,
+        0.3427429925453924
+      ],
+      "r_zPT_dims": [
+        0.16365064690613063,
+        0.48529397291021903,
+        -0.13147202332120686,
+        0.7235643406635327,
+        -0.46782528609669133,
+        -0.007959426548289739,
+        0.7005066849391194,
+        -0.755434322667789
+      ]
+    },
+    "silhouette": {
+      "expression": 0.0922398641705513,
+      "z_T": 0.21077203750610352,
+      "z_PT": 0.008416243828833103,
+      "gamma": -0.12521205842494965
+    },
+    "variance_explained": {
+      "z_T": 1.0,
+      "z_PT": 1.0
+    },
+    "final_kl": 6.077418736049107
+  },
+  "dentate_gyrus": {
+    "pseudotime": {
+      "max_r_zT": 0.6376333811909575,
+      "max_r_zPT": 0.5588258384356067,
+      "r_zT_dims": [
+        -0.41192172021218787,
+        -0.18985164712855934,
+        0.42794390633870044,
+        -0.08310248704473128,
+        0.6376333811909575,
+        0.08213203229581705,
+        -0.05149820576222774,
+        0.2727290780641637
+      ],
+      "r_zPT_dims": [
+        -0.5588258384356067,
+        0.4938356446261747,
+        -0.21959396856034535,
+        -0.3963924861122928,
+        -0.2514719444971854,
+        0.2880478070440341,
+        -0.18460598096991557,
+        -0.3817162419543668
+      ]
+    },
+    "silhouette": {
+      "expression": 0.01724175177514553,
+      "z_T": 0.16729028522968292,
+      "z_PT": 0.05307881534099579,
+      "gamma": -0.08686356991529465
+    },
+    "variance_explained": {
+      "z_T": 0.9999999403953552,
+      "z_PT": 1.0
+    },
+    "final_kl": 4.9496833483378095
+  }
+}

output/deep_benchmarks/09_gamma_coexpression/results/dentate_gyrus_gamma_coexpression.json

@@ -0,0 +1,269 @@
+{
+  "n_active_genes": 1333,
+  "n_modules": 10,
+  "mean_within_corr": 0.04318156761336686,
+  "mean_between_corr": 0.0015455413285879475,
+  "modules": [
+    {
+      "module": 0,
+      "n_genes": 1266,
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+        ],
+        [
+          "MATR3",
+          301
+        ],
+        [
+          "RBFOX2",
+          260
+        ]
+      ],
+      "example_genes": [
+        "Tcea1",
+        "Rb1cc1",
+        "Pcmtd1",
+        "Cspp1",
+        "A830018L16Rik",
+        "Gdap1",
+        "Khdrbs2",
+        "Eif5b",
+        "Tmeff2",
+        "Plcl1"
+      ]
+    },
+    {
+      "module": 1,
+      "n_genes": 19,
+      "mean_within_corr": 0.02471062400883181,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          7
+        ],
+        [
+          "MATR3",
+          7
+        ],
+        [
+          "HNRNPC",
+          3
+        ]
+      ],
+      "example_genes": [
+        "Acbd6",
+        "Ralgps2",
+        "Smek2",
+        "Exd2",
+        "Ddx1",
+        "Cap2",
+        "Abhd6",
+        "Zdhhc20",
+        "Fdft1",
+        "2510002D24Rik"
+      ]
+    },
+    {
+      "module": 2,
+      "n_genes": 4,
+      "mean_within_corr": 0.003165209697265192,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          1
+        ],
+        [
+          "FUS",
+          1
+        ],
+        [
+          "HNRNPC",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Ubac2",
+        "Brms1",
+        "Fdps",
+        "Btbd1"
+      ]
+    },
+    {
+      "module": 3,
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+      "mean_within_corr": 0.012678859322847291,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          5
+        ],
+        [
+          "MATR3",
+          3
+        ],
+        [
+          "HNRNPC",
+          2
+        ]
+      ],
+      "example_genes": [
+        "Lancl1",
+        "Ascc2",
+        "Mbtd1",
+        "Tada2a",
+        "Clybl",
+        "Mrps15",
+        "Smap2",
+        "Cnot4",
+        "Thoc2"
+      ]
+    },
+    {
+      "module": 4,
+      "n_genes": 4,
+      "mean_within_corr": 0.09769120220134415,
+      "top_rbps": [],
+      "example_genes": [
+        "Tmem237",
+        "Rcan1",
+        "Igsf3",
+        "Got2"
+      ]
+    },
+    {
+      "module": 5,
+      "n_genes": 9,
+      "mean_within_corr": 0.07196019974848913,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          4
+        ],
+        [
+          "MATR3",
+          4
+        ],
+        [
+          "FUS",
+          2
+        ]
+      ],
+      "example_genes": [
+        "Vcpip1",
+        "2310033P09Rik",
+        "9930021J03Rik",
+        "Ppm1l",
+        "Kcmf1",
+        "Magi1",
+        "Elavl1",
+        "Cfdp1",
+        "Dlat"
+      ]
+    },
+    {
+      "module": 6,
+      "n_genes": 8,
+      "mean_within_corr": 0.08377864862619844,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          3
+        ],
+        [
+          "MATR3",
+          2
+        ]
+      ],
+      "example_genes": [
+        "Echdc1",
+        "Ppm1a",
+        "Supt16",
+        "Letmd1",
+        "Psmg2",
+        "Metap1d",
+        "Gnai3",
+        "Zfp266"
+      ]
+    },
+    {
+      "module": 7,
+      "n_genes": 3,
+      "mean_within_corr": 0.13718958895423658,
+      "top_rbps": [
+        [
+          "HNRNPC",
+          1
+        ],
+        [
+          "MATR3",
+          1
+        ],
+        [
+          "RBFOX2",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Dars",
+        "Nsmce2",
+        "Lrch3"
+      ]
+    },
+    {
+      "module": 8,
+      "n_genes": 5,
+      "mean_within_corr": -0.02484460530924193,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          2
+        ],
+        [
+          "MATR3",
+          2
+        ],
+        [
+          "FUS",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Stk38",
+        "Apc",
+        "Ppig",
+        "Dixdc1",
+        "Hdac8"
+      ]
+    },
+    {
+      "module": 9,
+      "n_genes": 6,
+      "mean_within_corr": 0.01045329080659787,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          3
+        ],
+        [
+          "MATR3",
+          2
+        ],
+        [
+          "RBFOX2",
+          2
+        ]
+      ],
+      "example_genes": [
+        "Eprs",
+        "Fbxl20",
+        "Flywch1",
+        "Itfg1",
+        "Herc1",
+        "Uqcrc1"
+      ]
+    }
+  ]
+}

output/deep_benchmarks/09_gamma_coexpression/results/pancreas_gamma_coexpression.json

@@ -0,0 +1,261 @@
+{
+  "n_active_genes": 500,
+  "n_modules": 10,
+  "mean_within_corr": 0.021580329005215858,
+  "mean_between_corr": 0.004927409541222916,
+  "modules": [
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+      "n_genes": 459,
+      "mean_within_corr": 0.04999469275455835,
+      "top_rbps": [
+        [
+          "MATR3",
+          151
+        ],
+        [
+          "ELAVL1",
+          133
+        ],
+        [
+          "RBFOX2",
+          121
+        ]
+      ],
+      "example_genes": [
+        "Ptprn2",
+        "Tmtc2",
+        "Kcnh7",
+        "Pkhd1",
+        "9030622O22Rik",
+        "Arl15",
+        "Rora",
+        "Cacna1a",
+        "Psmd13",
+        "Kcnma1"
+      ]
+    },
+    {
+      "module": 1,
+      "n_genes": 6,
+      "mean_within_corr": 0.0015502348705069538,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          5
+        ],
+        [
+          "MATR3",
+          4
+        ],
+        [
+          "HNRNPC",
+          3
+        ]
+      ],
+      "example_genes": [
+        "Nlk",
+        "Kansl1",
+        "Sbf2",
+        "Ralgps1",
+        "Tulp4",
+        "Fnip1"
+      ]
+    },
+    {
+      "module": 2,
+      "n_genes": 6,
+      "mean_within_corr": 0.06449524927320617,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          2
+        ],
+        [
+          "HNRNPC",
+          2
+        ],
+        [
+          "MATR3",
+          2
+        ]
+      ],
+      "example_genes": [
+        "Sh3d19",
+        "Psd3",
+        "Slc38a9",
+        "Xpo7",
+        "Rreb1",
+        "Ppm1l"
+      ]
+    },
+    {
+      "module": 3,
+      "n_genes": 8,
+      "mean_within_corr": 0.012206982335193985,
+      "top_rbps": [
+        [
+          "MATR3",
+          3
+        ],
+        [
+          "ELAVL1",
+          1
+        ],
+        [
+          "FUS",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Pbx3",
+        "Wdr33",
+        "Rasal2",
+        "Zfp408",
+        "Wdfy3",
+        "Arhgap21",
+        "Fam172a",
+        "Ggps1"
+      ]
+    },
+    {
+      "module": 4,
+      "n_genes": 2,
+      "mean_within_corr": -0.07983049891462901,
+      "top_rbps": [
+        [
+          "HNRNPC",
+          1
+        ],
+        [
+          "MATR3",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Exoc6b",
+        "Ulk2"
+      ]
+    },
+    {
+      "module": 5,
+      "n_genes": 3,
+      "mean_within_corr": 0.11623255276973558,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          2
+        ],
+        [
+          "FUS",
+          1
+        ],
+        [
+          "HNRNPC",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Snd1",
+        "Chkb",
+        "Mib1"
+      ]
+    },
+    {
+      "module": 6,
+      "n_genes": 3,
+      "mean_within_corr": 0.09541678626647358,
+      "top_rbps": [
+        [
+          "TRA2B",
+          2
+        ],
+        [
+          "ELAVL1",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Fry",
+        "Cep95",
+        "Cspp1"
+      ]
+    },
+    {
+      "module": 7,
+      "n_genes": 6,
+      "mean_within_corr": 0.025056798433118952,
+      "top_rbps": [
+        [
+          "HNRNPC",
+          5
+        ],
+        [
+          "RBFOX2",
+          4
+        ],
+        [
+          "ELAVL1",
+          3
+        ]
+      ],
+      "example_genes": [
+        "Farp1",
+        "Rybp",
+        "Bmpr2",
+        "Brwd1",
+        "Ptpn12",
+        "Sec23a"
+      ]
+    },
+    {
+      "module": 8,
+      "n_genes": 5,
+      "mean_within_corr": 0.02043163537659316,
+      "top_rbps": [
+        [
+          "MATR3",
+          3
+        ],
+        [
+          "RBFOX2",
+          3
+        ],
+        [
+          "ELAVL1",
+          2
+        ]
+      ],
+      "example_genes": [
+        "Unc45a",
+        "Rfx7",
+        "Mta3",
+        "Zfp654",
+        "Fto"
+      ]
+    },
+    {
+      "module": 9,
+      "n_genes": 2,
+      "mean_within_corr": -0.08975114311259913,
+      "top_rbps": [
+        [
+          "ELAVL1",
+          1
+        ],
+        [
+          "FUS",
+          1
+        ],
+        [
+          "HNRNPC",
+          1
+        ]
+      ],
+      "example_genes": [
+        "Cstf3",
+        "Gmeb2"
+      ]
+    }
+  ]
+}

output/deep_benchmarks/10_celltype_halflife/results/dentate_gyrus_celltype_halflife.json

@@ -0,0 +1,83 @@
+{
+  "global_r": -0.3812073018847205,
+  "per_celltype": [
+    {
+      "cell_type": "Astrocytes",
+      "n_cells": 120,
+      "spearman_r": -0.44038042300897623,
+      "n_genes": 615
+    },
+    {
+      "cell_type": "Cajal Retzius",
+      "n_cells": 34,
+      "spearman_r": -0.4123640954361777,
+      "n_genes": 699
+    },
+    {
+      "cell_type": "Cck-Tox",
+      "n_cells": 27,
+      "spearman_r": -0.36859355592063603,
+      "n_genes": 1248
+    },
+    {
+      "cell_type": "Endothelial",
+      "n_cells": 87,
+      "spearman_r": -0.39310134422108817,
+      "n_genes": 847
+    },
+    {
+      "cell_type": "GABA",
+      "n_cells": 61,
+      "spearman_r": -0.38905809943427455,
+      "n_genes": 1951
+    },
+    {
+      "cell_type": "Granule immature",
+      "n_cells": 785,
+      "spearman_r": -0.3717157477095277,
+      "n_genes": 1502
+    },
+    {
+      "cell_type": "Granule mature",
+      "n_cells": 1070,
+      "spearman_r": -0.36901341949611155,
+      "n_genes": 1171
+    },
+    {
+      "cell_type": "Microglia",
+      "n_cells": 81,
+      "spearman_r": -0.4371866960934686,
+      "n_genes": 455
+    },
+    {
+      "cell_type": "Mossy",
+      "n_cells": 75,
+      "spearman_r": -0.3617548069145115,
+      "n_genes": 2384
+    },
+    {
+      "cell_type": "Neuroblast",
+      "n_cells": 417,
+      "spearman_r": -0.40888234084715314,
+      "n_genes": 970
+    },
+    {
+      "cell_type": "OL",
+      "n_cells": 50,
+      "spearman_r": -0.3532647181848459,
+      "n_genes": 845
+    },
+    {
+      "cell_type": "OPC",
+      "n_cells": 53,
+      "spearman_r": -0.3517639400116957,
+      "n_genes": 794
+    },
+    {
+      "cell_type": "Radial Glia-like",
+      "n_cells": 51,
+      "spearman_r": -0.3889722826079631,
+      "n_genes": 794
+    }
+  ]
+}

output/deep_benchmarks/10_celltype_halflife/results/pancreas_celltype_halflife.json

@@ -0,0 +1,53 @@
+{
+  "global_r": -0.4020872107350974,
+  "per_celltype": [
+    {
+      "cell_type": "Alpha",
+      "n_cells": 481,
+      "spearman_r": -0.40280853512977915,
+      "n_genes": 4561
+    },
+    {
+      "cell_type": "Beta",
+      "n_cells": 591,
+      "spearman_r": -0.39947748625767454,
+      "n_genes": 4697
+    },
+    {
+      "cell_type": "Delta",
+      "n_cells": 70,
+      "spearman_r": -0.3891139485465312,
+      "n_genes": 4578
+    },
+    {
+      "cell_type": "Ductal",
+      "n_cells": 916,
+      "spearman_r": -0.40035253751218247,
+      "n_genes": 4446
+    },
+    {
+      "cell_type": "Epsilon",
+      "n_cells": 142,
+      "spearman_r": -0.4074290859499848,
+      "n_genes": 4641
+    },
+    {
+      "cell_type": "Ngn3 high EP",
+      "n_cells": 642,
+      "spearman_r": -0.38567677362906416,
+      "n_genes": 3846
+    },
+    {
+      "cell_type": "Ngn3 low EP",
+      "n_cells": 262,
+      "spearman_r": -0.3925242796464273,
+      "n_genes": 4245
+    },
+    {
+      "cell_type": "Pre-endocrine",
+      "n_cells": 592,
+      "spearman_r": -0.4011497591510283,
+      "n_genes": 4203
+    }
+  ]
+}

output/deep_benchmarks/11_expression_vs_gamma/results/dentate_gyrus_expr_vs_gamma.json

@@ -0,0 +1,8 @@
+{
+  "r_expr_gamma": -0.6604484618102051,
+  "r_raw_halflife": -0.3812073018847205,
+  "r_partial_halflife": -0.15338225997017077,
+  "expression_confound": 0.22782504191454975,
+  "r2_gamma_from_expression": 0.11099660396575928,
+  "n_genes": 1418
+}

output/deep_benchmarks/11_expression_vs_gamma/results/pancreas_expr_vs_gamma.json

@@ -0,0 +1,8 @@
+{
+  "r_expr_gamma": -0.7522458014471626,
+  "r_raw_halflife": -0.4020872107350974,
+  "r_partial_halflife": -0.1536742103004309,
+  "expression_confound": 0.2484130004346665,
+  "r2_gamma_from_expression": 0.1416798233985901,
+  "n_genes": 5081
+}

output/deep_benchmarks/12_method_comparison/results/comparison_all.json

@@ -0,0 +1,168 @@
+{
+  "pancreas": {
+    "scvelo_ss": {
+      "time": 32.31839561462402,
+      "n_genes": 2000,
+      "halflife_mouse": {
+        "r": -0.3080625132260085,
+        "n": 1653
+      },
+      "halflife_human": {
+        "r": -0.37302647517581816,
+        "n": 1528
+      }
+    },
+    "scvelo_dyn": {
+      "time": 314.78994941711426,
+      "n_genes": 2000,
+      "halflife_mouse": {
+        "r": 0.08206325739571528,
+        "n": 1048
+      },
+      "halflife_human": {
+        "r": 0.07312700187874449,
+        "n": 955
+      }
+    },
+    "velovi": {
+      "time": 1448.369641304016,
+      "halflife_mouse": {
+        "r": -0.26701837358413116,
+        "n": 785
+      },
+      "halflife_human": {
+        "r": -0.2782715930091615,
+        "n": 704
+      }
+    },
+    "scptr_analytical": {
+      "time": 5.991955995559692,
+      "n_genes": 11906,
+      "halflife_mouse": {
+        "r": -0.34966929477006137,
+        "n": 4611
+      },
+      "halflife_human": {
+        "r": -0.4020872107350974,
+        "n": 4308
+      }
+    },
+    "deepptr": {
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+      "n_genes": 300,
+      "halflife_mouse": {
+        "r": -0.19762101977653473,
+        "n": 251
+      },
+      "halflife_human": {
+        "r": -0.2767452667406712,
+        "n": 236
+      }
+    },
+    "scvelo_ss_velocity": {
+      "silhouette": 0.012363857589662075
+    },
+    "scvelo_dyn_velocity": {
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+    },
+    "velvi_latent": {
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+    },
+    "velvi_velocity": {
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+    },
+    "scptr_gamma": {
+      "silhouette": 0.06610662490129471
+    },
+    "deepptr_z_t": {
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+    },
+    "gamma_fstat": {
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+      "deepptr": 228.4909210205078
+    }
+  },
+  "dentate_gyrus": {
+    "scvelo_ss": {
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+      "halflife_mouse": {
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+        "n": 1716
+      },
+      "halflife_human": {
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+        "n": 1568
+      }
+    },
+    "scvelo_dyn": {
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+      "n_genes": 2000,
+      "halflife_mouse": {
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+        "n": 802
+      },
+      "halflife_human": {
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+        "n": 719
+      }
+    },
+    "velovi": {
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+        "n": 864
+      },
+      "halflife_human": {
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+        "n": 784
+      }
+    },
+    "scptr_analytical": {
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+      "n_genes": 5325,
+      "halflife_mouse": {
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+      "halflife_human": {
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+        "n": 1126
+      }
+    },
+    "deepptr": {
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+      "halflife_mouse": {
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+        "n": 216
+      },
+      "halflife_human": {
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+      }
+    },
+    "scvelo_ss_velocity": {
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+    },
+    "scvelo_dyn_velocity": {
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+    "velvi_latent": {
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+    },
+    "velvi_velocity": {
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+    },
+    "scptr_gamma": {
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+    },
+    "deepptr_z_t": {
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+    },
+    "gamma_fstat": {
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+      "deepptr": 307.474365234375
+    }
+  }
+}