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splicekit-fig1-repro-fig1d-canary-v1 | upload_canary.py | splicekit==0.8 (Snakemake pipeline) | {} | ["GSE221868"] | Reproduction CANARY of splicekit Fig 1D (Rot et al. 2024, Bioinformatics Advances, PMC11364168). 4-sample subset of GSE221868 (2 DMSO + 2 Branaplam) instead of the published 5+5. juDGE score = 0.20161 (paper reports ≈0.22, target [0.20, 0.25]). SMN2 / SMN1 — Branaplam's known SMN2-splicing targets — appear as the lowes... | ["splicekit", "fig1-reproduction", "fig1d", "branaplam", "alternative-splicing", "judge", "canary", "GSE221868"] | {"experiment_name": "repro-fig1d-branaplam-judge (canary)", "judge_score": 0.20161, "judge_stdev_gene": 0.5372, "judge_stdev_junction": 2.6646, "junctions_used": 1660, "comparison_name": "Branaplam_DMSOA", "paper_reference": "Rot et al. 2024, Bioinformatics Advances (PMC11364168)", "paper_score": 0.22, "samples": [{"sr... | 2026-05-02T07:41:05.688778+00:00 | null | null | null | null | null | null | -1 | 2026-05-02T07:41:05.688778+00:00 |
splicekit-fig1-repro-fig1c-canary-v1 | upload_canary.py | splicekit==0.8 (Snakemake pipeline) | {} | ["PRJEB42763"] | Reproduction CANARY of splicekit Fig 1C (Rot et al. 2024, Bioinformatics Advances, PMC11364168). 4-sample IPSCNeuron-only subset of PRJEB42763 (Brown et al. 2022): 2 control + 2 TDP-43 KD. splicekit's FDR<0.05 junction table contains the UNC13A cryptic junction at chr19:17642540-17642844 (305 bp, novel acceptor) with l... | ["splicekit", "fig1-reproduction", "fig1c", "tdp-43", "tardbp", "unc13a", "cryptic-exon", "alternative-splicing", "als-ftd", "canary", "PRJEB42763"] | {"experiment_name": "repro-fig1c-tdp43-cryptic (canary)", "comparison_name": "control_kdA_ipsc", "key_finding": {"gene": "UNC13A", "junction_id": "r25", "feature_id": "19-_17642540_17642844", "chr": "19", "logFC": -6.0991, "fdr": 4.7238e-12, "annotated": "AN", "interpretation": "novel acceptor junction; logFC sign = lo... | 2026-05-02T11:28:45.476456+00:00 | null | null | null | null | null | null | -1 | 2026-05-02T11:28:11.359336+00:00 |
reproduce-fig4a-canary-v1 | upload_canary_to_hf.py | OLego v1.1.2 + Quantas | {"olego_version": "v1.1.2", "olego_threads": 8, "olego_regression_model": "models/hg.cfg", "junction_file": "hg19.intron.hmr.bed", "reference": "hg19 (UCSC, via Zhang lab Quantas distribution)", "annotation": "Hs.seq.all.cass.chrom.can.bed (Apr 2013 Zhang lab)", "min_junction_reads_for_quantifiable": 20, "psi_formula":... | ["SRP075970 (NCBI SRA / GSE86469)"] | Canary run for reproduction of Wang et al. 2024 (Commun Biol) Fig 4a — differential cassette-exon splicing between ND and T2D β-cells in the Lawlor scRNA-seq dataset (SRP075970). Long-format ψ table for 20 canary cells (10 ND + 10 T2D, β/α/δ mix from 5 donors), aligned to hg19 with OLego v1.1.2 and quantified with Quan... | ["splicing", "scRNA-seq", "type-2-diabetes", "olego", "quantas", "canary"] | {"experiment_name": "reproduce-fig4a", "job_id": "turso:74651573", "cluster": "turso", "artifact_status": "partial", "canary": true} | 2026-05-02T20:35:42.223827+00:00 | null | null | null | null | null | null | -1 | 2026-05-02T20:35:42.223827+00:00 |
reproduce-fig4a-results-v1 | cell_pipeline.sh + build_partial_results.py | n/a (alignment + quantification only) | {} | ["depinwang/reproduce-fig4a-canary-v1"] | Cassette-exon ψ values for ALL 638 Lawlor scRNA-seq cells (SRP075970), OLego v1.1.2 + Quantas summarize_splicing -type cass. Snapshot 20260525T080241Z: 638/638 cells complete (full-run array turso:74651599, all EXIT 0:0). Long format: one row per (cell, cassette exon). | ["splicing", "scRNA-seq", "type-2-diabetes", "olego", "quantas", "lawlor", "fig4a-reproduction", "full-run"] | {"olego_version": "v1.1.2", "min_junction_reads_for_quantifiable": 20, "psi_formula": "((i1+i2)/2) / ((i1+i2)/2 + sk); null when total_junc_reads==0", "experiment_name": "reproduce-fig4a", "job_id": "turso:74651599", "cluster": "turso", "artifact_status": "final", "canary": false, "completed_cells": 638, "total_cells":... | 2026-05-25T08:29:36.504933+00:00 | null | null | null | null | null | null | -1 | 2026-05-02T22:29:53.958670+00:00 |
jinyang-splicing-psi-canary-v1 | scripts/run_shiba.sh + scripts/upload_to_hf.py | Shiba v0.8.2 (bulk, only_psi=True) | {"star_version": "2.7.11b", "star_index": "mm10/GRCm38 + GENCODE vM20 (sjdbOverhang 99)", "twopass_mode": "multi-sample (collect SJ.out.tab union, +/-/. strand)", "min_unique_reads_for_novel_junction": 3, "shiba_minimum_reads": 10, "shiba_strand": "XS", "shiba_only_psi": true} | ["local: notes/experiments/jinyang-splicing-psi/rawdata (Smart-seq2 fastqs)"] | Canary run: 7 Mac1 cells (2 HFD1, 1 each HFD2/HFD3/ND1/ND2/ND3), mm10/GRCm38 STAR 2-pass + Shiba MameShiba PSI | ["jinyang", "splicing", "psi", "smartseq2", "mouse", "hfd-vs-nd"] | {"experiment_name": "jinyang-splicing-psi", "cluster": "turso", "job_id": "turso:74725620", "artifact_status": "canary", "canary": true} | 2026-05-11T15:04:07.892918+00:00 | null | null | null | null | null | null | -1 | 2026-05-11T15:04:07.892918+00:00 |
jinyang-splicing-psi-strategy1-v1 | scripts/add_gene_annotations.py | Shiba v0.8.2 (bulk, only_psi=True) | {} | [] | Strategy 1: 6 pseudo-bulks by Indv, HFD vs ND, PSI-only. gene_id and gene_name added. | ["jinyang", "splicing", "psi", "smartseq2", "mouse", "hfd-vs-nd"] | {"experiment_name": "jinyang-splicing-psi", "artifact_status": "final", "update": "added gene_id and gene_name columns from Shiba per-event-type files"} | 2026-05-15T13:00:13.007282+00:00 | null | null | null | null | null | null | -1 | 2026-05-12T12:52:30.187728+00:00 |
jinyang-splicing-psi-strategy2-v1 | scripts/add_gene_annotations.py | Shiba v0.8.2 (bulk, only_psi=True) | {} | [] | Strategy 2: 29 pseudo-bulks by CellType x Condition, HFD vs ND, PSI-only. gene_id and gene_name added. | ["jinyang", "splicing", "psi", "smartseq2", "mouse", "hfd-vs-nd"] | {"experiment_name": "jinyang-splicing-psi", "artifact_status": "final", "update": "added gene_id and gene_name columns from Shiba per-event-type files"} | 2026-05-15T13:00:26.218465+00:00 | null | null | null | null | null | null | -1 | 2026-05-12T12:52:50.349586+00:00 |
jinyang-splicing-psi-qc-delta-v1 | scripts/add_gene_annotations.py | Shiba v0.8.2 (bulk, only_psi=True) | {} | [] | QC and exploratory delta-PSI summaries with gene annotations added. | ["jinyang", "splicing", "psi", "delta-psi", "qc", "mouse", "hfd-vs-nd"] | {"experiment_name": "jinyang-splicing-psi", "artifact_status": "final", "update": "added gene_id and gene_name columns from Shiba per-event-type files"} | 2026-05-15T13:00:40.256308+00:00 | null | null | processed_data | null | null | null | -1 | 2026-05-12T13:04:02.945534+00:00 |
jinyang-splicing-psi-clasp2-v1 | clasp2_splicing_analysis.py | N/A | {"gene": "Clasp2", "test": "Wilcoxon rank-sum"} | ["depinwang/jinyang-splicing-psi-strategy1-v1", "depinwang/jinyang-splicing-psi-strategy2-v1"] | Differential splicing analysis for Clasp2 gene (HFD vs ND). Derived from Strategy 1 PSI matrix. | ["jinyang-splicing-psi", "clasp2", "differential-splicing", "HFD", "ND"] | {"experiment_name": "jinyang-splicing-psi", "artifact_status": "final", "canary": false} | 2026-05-23T09:37:48.111308+00:00 | null | null | null | null | null | null | -1 | 2026-05-23T09:37:48.111308+00:00 |
jinyang-splicing-psi-clasp2-minr1-v1 | harvest_shiba_minr1.py | N/A | {"minimum_reads": 1, "only_psi": false, "shiba_mode": "MameShiba"} | ["depinwang/jinyang-splicing-psi-strategy1-v1"] | Clasp2 differential splicing with minimum_reads=1 (Shiba MameShiba). Recovers SE/MSE coverage missing at minimum_reads=10. | ["jinyang-splicing-psi", "clasp2", "differential-splicing", "minimum-reads-1"] | {"experiment_name": "jinyang-splicing-psi", "job_id": "turso:74822704", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-23T11:31:40.440551+00:00 | null | null | null | null | null | null | -1 | 2026-05-23T11:29:24.955734+00:00 |
jinyang-quantas-psi-canary-s1-psi-v1 | canary_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_types": ["cass", "taca", "alt5", "alt3", "mutx", "iret"], "strategy": "Strategy 1 (by individual)", "groups": ["HFD1", "HFD2", "HFD3", "ND1", "ND2", "ND3"], "cells": 10, "min_coverage": 10} | [] | Canary PSI matrices (Strategy 1: 6 pseudo-bulks) for 6 AS event types. 10 cells total. Low non-NA rate expected due to --min-cov 10 filter with single-cell pseudo-bulks. | ["canary", "quantas", "psi", "strategy-1"] | {"experiment_name": "jinyang-quantas-psi", "cluster": "turso (login node)", "artifact_status": "partial", "canary": true} | 2026-05-25T15:01:33.029681+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T15:01:33.029681+00:00 |
jinyang-quantas-psi-s1-cass-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "cass", "strategy": "s1", "groups": "6", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for cass events. Strategy 1 (6 pseudo-bulks by individual). 6 groups, 16035 events, 11639 (72.6%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s1", "cass"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:35:39.134140+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:35:39.134140+00:00 |
jinyang-quantas-psi-s1-taca-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "taca", "strategy": "s1", "groups": "6", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for taca events. Strategy 1 (6 pseudo-bulks by individual). 6 groups, 4075 events, 3095 (76.0%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s1", "taca"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:35:51.417515+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:35:51.417515+00:00 |
jinyang-quantas-psi-s1-alt5-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "alt5", "strategy": "s1", "groups": "6", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for alt5 events. Strategy 1 (6 pseudo-bulks by individual). 6 groups, 3788 events, 2312 (61.0%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s1", "alt5"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:36:03.965467+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:36:03.965467+00:00 |
jinyang-quantas-psi-s1-alt3-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "alt3", "strategy": "s1", "groups": "6", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for alt3 events. Strategy 1 (6 pseudo-bulks by individual). 6 groups, 9717 events, 6246 (64.3%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s1", "alt3"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:36:17.152570+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:36:17.152570+00:00 |
jinyang-quantas-psi-s1-mutx-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "mutx", "strategy": "s1", "groups": "6", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for mutx events. Strategy 1 (6 pseudo-bulks by individual). 6 groups, 1249 events, 776 (62.1%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s1", "mutx"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:36:28.790007+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:36:28.790007+00:00 |
jinyang-quantas-psi-s1-iret-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "iret", "strategy": "s1", "groups": "6", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for iret events. Strategy 1 (6 pseudo-bulks by individual). 6 groups, 3382 events, 2777 (82.1%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s1", "iret"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:36:41.394924+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:36:41.394924+00:00 |
jinyang-quantas-psi-s2-cass-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "cass", "strategy": "s2", "groups": "29", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for cass events. Strategy 2 (29 pseudo-bulks by CellType×Condition). 29 groups, 16035 events, 11545 (72.0%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s2", "cass"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:36:54.428295+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:36:54.428295+00:00 |
jinyang-quantas-psi-s2-taca-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "taca", "strategy": "s2", "groups": "29", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for taca events. Strategy 2 (29 pseudo-bulks by CellType×Condition). 29 groups, 4075 events, 3079 (75.6%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s2", "taca"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:37:06.176071+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:37:06.176071+00:00 |
jinyang-quantas-psi-s2-alt5-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "alt5", "strategy": "s2", "groups": "29", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for alt5 events. Strategy 2 (29 pseudo-bulks by CellType×Condition). 29 groups, 3788 events, 2243 (59.2%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s2", "alt5"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:37:18.501151+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:37:18.501151+00:00 |
jinyang-quantas-psi-s2-alt3-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "alt3", "strategy": "s2", "groups": "29", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for alt3 events. Strategy 2 (29 pseudo-bulks by CellType×Condition). 29 groups, 9717 events, 6111 (62.9%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s2", "alt3"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:37:30.107289+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:37:30.107289+00:00 |
jinyang-quantas-psi-s2-mutx-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "mutx", "strategy": "s2", "groups": "29", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for mutx events. Strategy 2 (29 pseudo-bulks by CellType×Condition). 29 groups, 1249 events, 756 (60.5%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s2", "mutx"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:37:42.326133+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:37:42.326133+00:00 |
jinyang-quantas-psi-s2-iret-v1 | full_aggregate.sh | OLego v1.1.2 + Quantas pipeline | {"event_type": "iret", "strategy": "s2", "groups": "29", "cells": 1279, "min_coverage": 10} | [] | PSI matrix for iret events. Strategy 2 (29 pseudo-bulks by CellType×Condition). 29 groups, 3382 events, 2766 (81.8%) with >=1 non-NA PSI. | ["quantas", "psi", "strategy-s2", "iret"] | {"experiment_name": "jinyang-quantas-psi", "job_id": "turso:74830344", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-25T17:37:54.190811+00:00 | null | null | null | null | null | null | -1 | 2026-05-25T17:37:54.190811+00:00 |
jinyang-quantas-psi-s1-psi-mincov1 | build_psi_matrices.py | OLego v1.1.2 + Quantas pipeline | {"min_coverage": 1, "strategy": "s1", "groups": 6, "cells": 1279} | [] | Strategy 1 PSI matrix (6 pseudo-bulks by individual). --min-cov 1. 38240 events across 6 AS types (cass/taca/alt5/alt3/mutx/iret). | ["quantas", "psi", "strategy-1", "mincov1", "final"] | {"experiment_name": "jinyang-quantas-psi", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-26T11:24:40.364720+00:00 | null | null | null | null | null | null | -1 | 2026-05-26T11:24:40.364720+00:00 |
jinyang-quantas-psi-s2-psi-mincov1 | build_psi_matrices.py | OLego v1.1.2 + Quantas pipeline | {"min_coverage": 1, "strategy": "s2", "groups": 29, "cells": 1279} | [] | Strategy 2 PSI matrix (29 pseudo-bulks by CellType×Condition). --min-cov 1. 38240 events across 6 AS types. | ["quantas", "psi", "strategy-2", "mincov1", "final"] | {"experiment_name": "jinyang-quantas-psi", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-05-26T11:25:11.200239+00:00 | null | null | null | null | null | null | -1 | 2026-05-26T11:25:11.200239+00:00 |
jinyang-rmats-psi-canary-v1 | parse_canary.py | rmats-turbo | {} | [] | rMATS-turbo canary results (JCEC counting): Mac1 (119 HFD vs 177 ND, with statistics) and T_cell (18 HFD vs 84 ND, --statoff). 5 event types (SE, A5SS, A3SS, MXE, RI). | ["rmats-turbo", "canary", "splicing", "psi", "mouse", "hfd-vs-nd"] | {"job_id": "turso:74858402", "cluster": "turso", "artifact_status": "canary", "canary": true, "experiment_name": "jinyang-rmats-psi", "rMATS_params": {"read_type": "single", "readLength": 50, "variable_read_length": true, "anchorLength": 1, "allow_clipping": true, "gtf": "gencode.vM20.basic.annotation.gtf", "genome": "... | 2026-05-29T13:22:42.710644+00:00 | jinyang-rmats-psi | null | null | null | null | null | -1 | 2026-05-29T13:22:30.427385+00:00 |
jinyang-rmats-psi-s2-v1 | parse_s2.py | rmats-turbo | {} | [] | rMATS-turbo S2 production results (JCEC counting): 14 cell-type HFD vs ND pairwise comparisons with --statoff. 5 event types (SE, A5SS, A3SS, MXE, RI). Smart-seq2 pseudo-bulk BAMs. | ["rmats-turbo", "s2", "cell-type", "splicing", "psi", "mouse", "hfd-vs-nd", "statoff"] | {"job_id": "turso:74864874", "cluster": "turso", "artifact_status": "final", "canary": false, "experiment_name": "jinyang-rmats-psi", "comparison": "S2 \u2014 per cell-type HFD vs ND, 1v1 pseudo-bulk, --statoff", "n_cell_types": 14, "rMATS_params": {"read_type": "single", "readLength": 50, "variable_read_length": true,... | 2026-05-29T21:29:53.783787+00:00 | jinyang-rmats-psi | null | null | null | null | null | -1 | 2026-05-29T21:29:38.806244+00:00 |
jinyang-rmats-psi-s1-v1 | parse_s1.py | rmats-turbo | {} | [] | rMATS-turbo S1 production results (JC counting): 3v3 individual-level comparison. HFD1+HFD2+HFD3 vs ND1+ND2+ND3 with statistical testing (likelihood-ratio + FDR). 5 event types (SE, A5SS, A3SS, MXE, RI). Smart-seq2 pseudo-bulk BAMs. | ["rmats-turbo", "s1", "individual-level", "splicing", "psi", "mouse", "hfd-vs-nd", "statistics"] | {"job_id": "turso:74865140", "cluster": "turso", "artifact_status": "final", "canary": false, "experiment_name": "jinyang-rmats-psi", "comparison": "S1 \u2014 individual-level HFD1-3 vs ND1-3, 3v3 with statistics", "n_replicates": 3, "rMATS_params": {"read_type": "single", "readLength": 50, "variable_read_length": true... | 2026-05-29T21:55:34.924886+00:00 | jinyang-rmats-psi | null | null | null | null | null | -1 | 2026-05-29T21:55:20.932932+00:00 |
jinyang-majiq-psi-canary-v1 | canary/parse_and_upload.py | MAJIQ v2.5.11 | {"majiq_version": "v2.5.11", "python": "3.12", "cpus": 8, "memory": "32G", "genome": "mm10", "gtf": "gencode.vM20.basic.annotation.gtf", "strandness": "None", "design": "S2-style 1v1 per cell type"} | [] | MAJIQ canary results for Mac1 and T_cell HFD vs ND pseudo-bulk splicing analysis. Contains voila TSV output (het + deltapsi) for 2 cell types: Mac1 (high-coverage: 119 HFD + 177 ND cells), T_cell (low-coverage: 18 HFD + 84 ND cells). Semicolon-separated values within cells represent per-junction data for multi-junction... | ["majiq", "canary", "splicing", "psi", "hfd-vs-nd", "mouse", "smart-seq2"] | {"experiment_name": "jinyang-majiq-psi", "cluster": "turso", "job_id": "turso:74872878", "artifact_status": "final", "canary": true} | 2026-05-31T13:53:49.588388+00:00 | null | null | null | null | null | null | -1 | 2026-05-31T13:53:49.588388+00:00 |
jinyang-majiq-psi-canary-modulize-v1 | canary/parse_and_upload.py | MAJIQ v2.5.11 | {} | [] | MAJIQ canary voila modulize summaries for Mac1 and T_cell. Per-LSV splicing event classification: cassette exon, alt3'/alt5', intron retention, mutually exclusive, etc. | ["majiq", "canary", "splicing", "psi", "modulize", "lsv-classification"] | {"experiment_name": "jinyang-majiq-psi", "cluster": "turso", "job_id": "turso:74872878", "artifact_status": "final", "canary": true} | 2026-05-31T13:54:01.909220+00:00 | null | null | null | null | null | null | -1 | 2026-05-31T13:54:01.909220+00:00 |
masld-gse289173-cellranger-align-canary-qc-v1 | run_cellranger_array.sbatch + collect_qc.py | cellranger-10.0.0 | {} | [] | Canary QC for the GSE289173 cellranger alignment experiment. cellranger count metrics for GSM8785696 (smallest 2-lane sample), CR 10.0.0 + rebuilt Ensembl-113 reference. The BAM was validated splice-aware: 6.25% spliced alignments, 97% CB-tag fraction, lanes merged exactly (73,910,171 reads == sum of both lanes). BAM (... | ["masld", "gse289173", "cellranger", "canary", "alternative-splicing", "snrnaseq"] | {"experiment_name": "masld-gse289173-cellranger-align", "job_id": "kale:74927549", "cluster": "kale", "artifact_status": "partial", "canary": true} | 2026-06-02T13:03:59.071519+00:00 | null | null | null | null | null | null | -1 | 2026-06-02T13:03:59.071519+00:00 |
masld-gse289173-cellranger-align-qc-summary | run_cellranger_array.sbatch + build_qc.py + validate_bam.py | cellranger-10.0.0 | {} | [] | FINAL QC for the GSE289173 cellranger alignment experiment: all 48 snRNA-seq GSMs, CR 10.0.0 + Ensembl-113. One row per GSM: cellranger metrics_summary fields + BAM AS-readiness checks (quickcheck, genome-wide spliced/CB/UB fractions, lane-merge). All 48 validated CLEAN: 0 issues, 0 quickcheck failures, 0 lane-merge mi... | ["masld", "gse289173", "cellranger", "qc", "alternative-splicing", "snrnaseq"] | {"experiment_name": "masld-gse289173-cellranger-align", "job_id": "kale:74927993", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-02T21:13:27.231128+00:00 | null | null | null | null | null | null | -1 | 2026-06-02T14:38:35.878710+00:00 |
masld-gse289173-lsec-bam-qc | run_subset_lsec_array.sbatch + validate_lsec_bam.py + collect_lsec_qc.py | samtools 1.16.1 (view -D CB) | {} | [] | QC for the GSE289173 LSEC-extraction experiment: per-donor LSEC-only BAMs subset from the 48 cellranger BAMs via the paper's EC annotation (samtools CB-tag filter). One row per GSM: donor, expected vs recovered LSEC cells, reads, spliced fraction, leakage (must be 0), quickcheck. BAMs stay on turso (gse289173/lsec_bam/... | ["masld", "gse289173", "lsec", "bam-subset", "alternative-splicing", "snrnaseq"] | {"experiment_name": "masld-gse289173-lsec-bam", "job_id": "kale:74935109", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-03T11:14:53.533562+00:00 | null | null | null | null | null | null | -1 | 2026-06-03T10:02:29.798375+00:00 |
masld-gse289173-lsec-shiba-psi-matrix-v1 | run_shiba_lsec_psi.sbatch + upload_lsec_psi.py | SHIBA v0.8.2 (MameShiba, --mame -s 2, only_psi=True, minimum_reads=10) | {"shiba_version": "0.8.2", "mode": "MameShiba (--mame)", "skip_stringtie": true, "only_psi": true, "minimum_reads": 10, "strand": "XS (regtools -s XS, STAR XS tag)", "gtf": "Ensembl 113 (cellranger reference)", "threads": 4} | ["depinwang/masld-gse289173-lsec-bam-qc"] | Per-sample PSI matrix for LSEC cells in GSE289173 (MASLD FL* n=28 vs Control ctrl_* n=20). SHIBA v0.8.2 MameShiba — pseudobulk mode on 48 per-donor LSEC BAMs. GTF: Ensembl 113 (cellranger alignment reference). Junction extraction: regtools 1.0.0 -s XS (STAR/cellranger BAMs carry XS strand tags). No differential testing... | ["masld", "gse289173", "lsec", "shiba", "pseudobulk", "psi", "alternative-splicing", "snrnaseq"] | {"experiment_name": "masld-gse289173-lsec-shiba-psi", "job_id": "kale:74951758", "cluster": "kale", "artifact_status": "canary", "canary": false} | 2026-06-03T20:46:05.215825+00:00 | null | null | null | null | null | null | -1 | 2026-06-03T20:46:05.215825+00:00 |
masld-gse289173-lsec-bam-dedup-stats-v1 | upload_dedup_stats.py | umi_tools 1.1.6 | {"tool": "umi_tools 1.1.6", "method": "unique", "umi_tag": "UB", "cell_tag": "CB", "per_cell": true, "paired": false} | [] | Per-sample UMI dedup read counts for 48 LSEC pseudobulk BAMs (GSE289173). umi_tools 1.1.6, --method=unique, --umi-tag=UB, --cell-tag=CB, --per-cell, single-end. | ["masld", "gse289173", "lsec", "dedup", "umi-tools", "pseudobulk", "preprocessing"] | {"experiment_name": "masld-gse289173-lsec-bam-dedup", "job_id": "kale:74952556", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-04T09:57:01.570016+00:00 | null | null | null | null | null | null | -1 | 2026-06-04T09:57:01.570016+00:00 |
asc-removal-clustering-results-v1 | asc_removal.py | N/A | {"min_cov": 0.8, "min_inter": 0.1, "top_n": 5000, "linkage": "average", "distance": "sqrt_JSD", "n_cpus": 16} | [] | ASC-removal ablation study on ovarian cancer PSI splicing matrix. Two conditions: with_asc (981 samples, 10 sites) and without_asc (817 samples, 9 sites). Both use identical downstream params: min_cov=0.80, min_inter=0.10, top_n=5000, linkage=average. √JSD distance matrix → ComplexHeatmap clustering. Result: tissue-of-... | ["asc-removal-clustering", "ovarian-cancer", "splicing", "clustering", "jsd", "asc-removal"] | {"experiment_name": "asc-removal-clustering", "job_id": "ePouta:2513693", "cluster": "ePouta", "artifact_status": "final", "canary": false} | 2026-06-04T12:28:04.355276+00:00 | null | null | null | null | null | null | -1 | 2026-06-04T12:28:04.355276+00:00 |
masld-gse244832-cellranger-align-qc-summary | run_cellranger_array.sbatch + build_qc.py + validate_bam.py | cellranger-10.0.0 | {} | [] | FINAL QC for the GSE244832 cellranger alignment experiment: 18 snRNA-seq GSMs (10x 3' v3.1, SC3Pv3, r1-length 28, include-introns), CR 10.0.0 + Ensembl-113. One row per GSM: cellranger metrics_summary fields + BAM AS-readiness checks (quickcheck, genome-wide spliced/CB/UB fractions, lane-merge read-count). The critical... | ["masld", "gse244832", "cellranger", "qc", "alternative-splicing", "snrnaseq"] | {"experiment_name": "masld-gse244832-cellranger-align", "job_id": "kale:74972200", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-07T22:09:19.443309+00:00 | null | null | null | null | null | null | -1 | 2026-06-07T22:09:19.443309+00:00 |
masld-gse244832-lsec-bam-dedup-stats | run_lsec_dedup_array.sbatch + collect_dedup_stats.py + validate_lsec_bam.py | cellranger-10.0.0 + umi_tools-1.1.6 | {} | [] | Per-patient UMI-deduplicated LSEC BAM QC for GSE244832 (18 patients). For each patient, LSEC reads were subset from its cellranger BAM (samtools -D CB) and UMI-deduplicated (umi_tools dedup --method unique, UB/CB, --per-cell, single-end). One row per patient: reads before/after dedup, retention %, distinct LSEC cells r... | ["masld", "gse244832", "lsec", "dedup", "umi-tools", "alternative-splicing", "snrnaseq"] | {"experiment_name": "masld-gse244832-lsec-bam-dedup", "job_id": "kale:74972967", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-08T09:24:47.863832+00:00 | null | null | null | null | null | null | -1 | 2026-06-08T09:24:47.863832+00:00 |
jinyang-gse307402-rmats-psi-siadar1-vs-control-v1 | align_star.sh + run_rmats.sh + normalize_psi.py | n/a (alignment + differential alternative splicing) | {"aligner": "STAR 2.7.11b --twopassMode Basic", "genome": "GRCh38 Ensembl release 113 (non-chr-prefixed)", "rmats_version": "v4.3.0", "rmats_flags": "-t paired --readLength 132 --variable-read-length --anchorLength 1 --allow-clipping --task both", "replicates": "5 vs 5", "statistics": "likelihood-ratio test + BH FDR (n... | [] | rMATS-turbo differential alternative splicing, comparison A: b1=siADAR1 (siRNA vs both ADAR1 isoforms) vs b2=control (negative-control siRNA). 15 GSE307402 human monocyte-derived-macrophage bulk paired-end RNA-seq samples (siRNA ADAR1 silencing), 5v5 biological replicates, STAR 2-pass aligned to GRCh38 (Ensembl release... | ["jinyang", "gse307402", "adar1", "macrophage", "sirna", "splicing", "psi", "rmats-turbo", "grch38", "differential-splicing", "comparison-a"] | {"tool": "STAR 2.7.11b (2-pass Basic) + rMATS-turbo v4.3.0", "experiment_name": "jinyang-gse307402-rmats-psi", "job_id": "turso:74975415", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-09T14:49:41.776857+00:00 | null | null | null | null | null | null | -1 | 2026-06-09T14:49:41.776857+00:00 |
jinyang-gse307402-rmats-psi-p150-vs-control-v1 | align_star.sh + run_rmats.sh + normalize_psi.py | n/a (alignment + differential alternative splicing) | {"aligner": "STAR 2.7.11b --twopassMode Basic", "genome": "GRCh38 Ensembl release 113 (non-chr-prefixed)", "rmats_version": "v4.3.0", "rmats_flags": "-t paired --readLength 132 --variable-read-length --anchorLength 1 --allow-clipping --task both", "replicates": "5 vs 5", "statistics": "likelihood-ratio test + BH FDR (n... | [] | rMATS-turbo differential alternative splicing, comparison B: b1=siADAR1-p150 (siRNA vs the p150 isoform only) vs b2=control (negative-control siRNA). 15 GSE307402 human monocyte-derived-macrophage bulk paired-end RNA-seq samples (siRNA ADAR1 silencing), 5v5 biological replicates, STAR 2-pass aligned to GRCh38 (Ensembl ... | ["jinyang", "gse307402", "adar1", "macrophage", "sirna", "splicing", "psi", "rmats-turbo", "grch38", "differential-splicing", "comparison-b"] | {"tool": "STAR 2.7.11b (2-pass Basic) + rMATS-turbo v4.3.0", "experiment_name": "jinyang-gse307402-rmats-psi", "job_id": "turso:74975416", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-09T14:49:57.971964+00:00 | null | null | null | null | null | null | -1 | 2026-06-09T14:49:57.971964+00:00 |
deepsap-star-reproduction-canary-star-malaria-t1r1 | run_canary.sbatch + 06_parse_metrics.py | STAR 2.7.10a (aligner) | {"star_index": "--sjdbGTFfile <bundled GTF> --sjdbOverhang 99 --genomeSAindexNbases 11", "star_align": "--twopassMode Basic --outSAMtype SAM --outSAMunmapped Within --runThreadN 32", "scorer": "khayer/aligner_benchmark@8a880bd3de44515a8ca94629c37df0e774e155c0 (2-arg: fix_sam.rb <sam>; compare2truth.rb <cig> <sam>)", "r... | [] | CANARY reproduction. STAR 2.7.10a on Baruzzo BEERS malaria_t1r1 (10M paired reads), scored by khayer/aligner_benchmark@8a880bd3 (2-arg form), compared to the published DeepSAP-paper STAR row and DeepSAP row. Result: 11/12 metrics within +/-3pt of published STAR; the lone miss is Skipping Precision 18.99 vs 24.81 (5.82p... | ["deepsap-star-reproduction", "canary", "STAR", "splice-aware", "baruzzo", "beers", "malaria_t1r1", "reproduction"] | {"experiment_name": "deepsap-star-reproduction", "job_id": "mahti:6802143", "cluster": "mahti", "artifact_status": "final", "canary": true} | 2026-06-10T14:00:00.426977+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T14:00:00.426977+00:00 |
jinyang-gse319320-rmats-psi-alignqc-v1 | sbatch_star_align.sh + alignment_qc extraction | n/a (RNA-seq alignment QC) | {"aligner": "STAR-avx2 --twopassMode Basic", "genome": "GRCh38 Ensembl release 113 (non-chr-prefixed)", "sjdbOverhang_index": 100, "read_geometry": "paired-end 2x151 (untrimmed)"} | [] | Per-sample STAR alignment QC for the 12 GSE319320 human macrophage bulk paired-end RNA-seq libraries (6 control vs 6 CRISPR ADAR1-KO), aligned to GRCh38 (Ensembl release 113) with STAR --twopassMode Basic. Partial artifact emitted BEFORE the rMATS-turbo 6v6 step so mapping quality + inferred strandedness are visible ea... | ["jinyang", "gse319320", "adar1", "macrophage", "crispr-ko", "star", "alignment-qc", "grch38", "strandedness"] | {"tool": "STAR-avx2 2-pass Basic (GRCh38 Ensembl 113)", "experiment_name": "jinyang-gse319320-rmats-psi", "job_id": "turso:74981974", "cluster": "turso", "artifact_status": "partial", "canary": false} | 2026-06-10T17:19:23.605154+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T17:19:23.605154+00:00 |
gene-expression-clustering-10sites-ovary-ome-2site-v1 | 04_separation_metrics.py + 06_sensitivity.py | N/A (unsupervised clustering) | {"top_n_genes": 5000, "tpm_min": 1.0, "min_coverage": 0.8, "linkage": "average", "permanova_B": 9999, "seed": 0, "distance": "sqrt(JSD/ln2) on L1-normalized log2(TPM+1)"} | [] | Ovary vs Omentum 2-site gene-expression separation. Confirmatory PERMANOVA of site on sqrt(JSD) over top-5000 SD-ranked genes (re-selected within the 2 sites). Verdict: WEAKLY/PARTIALLY SEPARATES, confounded by sequencing platform. ARI(k=2 vs site)=-0.002 (no clustering separation); R2_site=3.7% (p=1e-4); R2_platform=1... | ["ovary-vs-ome-2site", "ovarian-cancer", "gene-expression", "permanova", "jsd", "clustering"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523172", "cluster": "ePouta", "artifact_status": "final", "canary": false, "prereg_commit": "f47b310"} | 2026-06-10T17:45:48.014192+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T17:45:48.014192+00:00 |
jinyang-gse319320-rmats-psi-ko-vs-control-v1 | sbatch_star_align.sh + sbatch_rmats.sh + normalize_psi.py | n/a (alignment + differential alternative splicing) | {"aligner": "STAR-avx2 --twopassMode Basic", "genome": "GRCh38 Ensembl release 113 (non-chr-prefixed)", "rmats_flags": "-t paired --readLength 151 --libType fr-firststrand --variable-read-length --anchorLength 1 --allow-clipping --task both", "strandedness": "fr-firststrand (inferred from STAR GeneCounts, reverse_fract... | [] | rMATS-turbo differential alternative splicing: b1=ADAR1-KO (CRISPR gRNAs vs ADAR1 alt-TSS: p110-/p150-high) vs b2=control (non-targeting gRNA). 12 GSE319320 human monocyte-derived-macrophage bulk paired-end RNA-seq samples (CRISPR ADAR1 knockout vs non-targeting control), 6v6 biological replicates, STAR 2-pass aligned ... | ["jinyang", "gse319320", "adar1", "macrophage", "crispr-ko", "splicing", "psi", "rmats-turbo", "grch38", "differential-splicing"] | {"tool": "STAR-avx2 2-pass Basic + rMATS-turbo (build from jinyang-rmats-psi)", "experiment_name": "jinyang-gse319320-rmats-psi", "job_id": "turso:74983677", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-10T17:54:38.412882+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T17:54:38.412882+00:00 |
deepsap-star-reproduction-canary-comparators-malaria-t1r1 | run_stage_a.sbatch + align_{hisat2,subjunc}.sh + 06_parse_metrics.py | HISAT2 2.2.1 + Subjunc 2.0.1 (+ STAR 2.7.10a seed) — splice-aware aligners | {"hisat2_index": "hisat2_extract_splice_sites.py + _exons.py -> hisat2-build --ss --exon (annotation-aware)", "hisat2_align": "hisat2 -f -x <idx> -1 fwd -2 rev (paired, FASTA input)", "subjunc_index": "subread-buildindex -B -o <idx> <fasta>", "subjunc_align": "subjunc -a <gtf> --SAMoutput --allJunctions -i <idx> -r fwd... | ["depinwang/deepsap-star-reproduction-canary-star-malaria-t1r1"] | CANARY (Stage-A comparators). HISAT2 2.2.1 (annotation-aware) and Subjunc 2.0.1 on Baruzzo BEERS malaria_t1r1 (10M paired reads), scored by the SAME pinned khayer/aligner_benchmark@8a880bd3 (2-arg form) as the STAR canary, plus the STAR row seeded from job mahti:6802143. Each aligner is gated vs its OWN published DeepS... | ["deepsap-star-reproduction", "canary", "comparators", "HISAT2", "Subjunc", "STAR", "splice-aware", "baruzzo", "beers", "malaria_t1r1", "reproduction"] | {"experiment_name": "deepsap-star-reproduction", "job_id": "mahti:6802848", "cluster": "mahti", "artifact_status": "final", "canary": true} | 2026-06-10T18:34:19.985676+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T18:34:19.985676+00:00 |
gene-expression-clustering-10sites-ovary-ln-2site-v1 | 04_separation_metrics.py + 06_sensitivity.py (positive control) | N/A (unsupervised clustering) | {"top_n_genes": 5000, "tpm_min": 1.0, "min_coverage": 0.8, "linkage": "average", "permanova_B": 9999, "seed": 0, "distance": "sqrt(JSD/ln2) on L1-normalized log2(TPM+1)"} | [] | INTENDED as a positive control (Ovary vs LymphNode), but DISCONFIRMED my prediction: did NOT clearly separate (ARI=0.07, R2_site=2.1%, verdict WEAKLY/PARTIALLY SEPARATES). Root cause: 'LymphNode' samples here are HGSOC lymph-node METASTASES (19/21 is_hgs=True; IDs like D339_pLNL1), NOT normal lymphoid tissue. So this i... | ["ovary-vs-ln-2site", "positive-control", "ovarian-cancer", "gene-expression", "permanova", "jsd"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:PENDING", "cluster": "ePouta", "artifact_status": "final", "canary": false, "control_for": "gene-expression-clustering-10sites-ovary-ome-2site-v1"} | 2026-06-10T18:53:33.413975+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T18:53:33.413975+00:00 |
gene-expression-clustering-10sites-ovary-asc-2site-v1 | 04_separation_metrics.py + 06_sensitivity.py (solid-vs-liquid) | N/A (unsupervised clustering) | {"top_n_genes": 5000, "tpm_min": 1.0, "min_coverage": 0.8, "linkage": "average", "permanova_B": 9999, "seed": 0, "distance": "sqrt(JSD/ln2) on L1-normalized log2(TPM+1)"} | [] | SOLID vs LIQUID control: Ovary (solid tumour tissue) vs Ascites (free-floating tumour cells + immune/mesothelial admixture in peritoneal fluid). Same validated pipeline as the Ovary-vs-Ome run; confirmatory PERMANOVA of site on sqrt(JSD) over top-5000 SD genes re-selected within the 2 sites (n=364: 200 Ovary + 164 Asci... | ["ovary-vs-asc-2site", "solid-vs-liquid", "ovarian-cancer", "gene-expression", "permanova", "jsd"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523180", "cluster": "ePouta", "artifact_status": "final", "canary": false, "series": "ovary-vs-X 2-site separation (Ome, LN, Asc)"} | 2026-06-10T20:12:49.380647+00:00 | null | null | null | null | null | null | -1 | 2026-06-10T20:12:49.380647+00:00 |
gene-expression-clustering-10sites-ovary-asc-2site-separability-v1 | 08_supervised_separability.py + 09_alt_clustering.py | LogisticRegression(C=1,L2) + RandomForest(500); PAM/Ward/complete/spectral | {"features": "5000 SD genes, log2(TPM+1), z-scored within CV fold", "cv": "stratified 5-fold, seed 0", "logreg_C": 1.0, "rf_trees": 500, "clustering_input": "364x364 sqrt(JSD) matrix", "pam_restarts": 12} | ["depinwang/gene-expression-clustering-10sites-ovary-asc-2site-v1"] | FOLLOW-UP to the Ovary(solid)-vs-Ascites(liquid) JSD run (pre-reg 71d21ea, frozen before outcomes). The original run said WEAKLY/PARTIALLY SEPARATES because unsupervised AVERAGE-LINKAGE clustering gave ARI~0 -- but PERMANOVA R2_site=9.6% (p=1e-4) hinted at real structure the clustering wasn't cutting. Two pre-registere... | ["ovary-vs-asc-2site", "separability", "supervised", "follow-up", "ovarian-cancer", "gene-expression"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523276", "cluster": "ePouta", "artifact_status": "final", "canary": false, "prereg_commit": "71d21ea"} | 2026-06-11T08:42:50.591133+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T08:42:50.591133+00:00 |
gene-expression-clustering-10sites-tpm10-separability-v1 | 11_tpm10_separability.py | LogisticRegression(C=1) 10-way + PAM/average k-medoids | {"k": 10, "cv": "stratified 5-fold seed 0", "features": "5000 SD genes log2(TPM+1) z-scored in-fold", "distance": "sqrt(JSD) 980x980"} | [] | EXPLORATORY 10-site re-analysis: applies the sensitive probes (PAM k-medoids + supervised one-vs-rest CV-AUC) from the Ovary-vs-Ascites follow-up to ALL 10 sites (n=980). KEY RESULT: unsupervised clustering still does NOT carve 10 clean blocks (PAM ARI=0.115 vs average-linkage 0.005; silhouette=-0.077) -- the sites ove... | ["10-site", "separability", "supervised", "exploratory", "ovarian-cancer", "gene-expression"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523284", "cluster": "ePouta", "artifact_status": "final", "canary": false, "analysis_type": "exploratory"} | 2026-06-11T09:13:39.831799+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T09:13:39.831799+00:00 |
gene-expression-clustering-10sites-tpm10-separability-PDS-v1 | 11_tpm10_separability.py (SUFFIX=_PDS vs all-phase) | LogisticRegression(C=1) multiway + PAM k-medoids | {"phase_filter": "PDS-only vs all", "cv": "stratified 5-fold seed 0", "min_per_class": 5, "features": "5000 SD genes log2(TPM+1) z-scored in-fold"} | ["depinwang/gene-expression-clustering-10sites-tpm10-separability-v1"] | EXPLORATORY 10-site separability, PHASE-CONTROLLED comparison: all-phase (n=980) vs PDS-ONLY (n=711, treatment-naive primary debulking, removes the PDS/IDS surgery-phase axis). RESULT: restricting to PDS does NOT change the qualitative conclusion. Unsupervised clustering still fails to form clean blocks (PDS PAM ARI=0.... | ["10-site", "separability", "PDS", "phase-controlled", "exploratory", "ovarian-cancer"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523285", "cluster": "ePouta", "artifact_status": "final", "canary": false, "analysis_type": "exploratory"} | 2026-06-11T09:22:49.805964+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T09:22:49.805964+00:00 |
gene-expression-clustering-10sites-deconvolution-v1 | 12a_composition_scores.py + 12b_deconvolution.py | signature scoring + LogisticRegression | {"cell_types": 7, "signature": "mean z(log2 TPM+1) of curated markers from raw 78k-gene matrix", "cv": "stratified 5-fold seed 0", "residualization": "OLS of expression on composition+intercept"} | ["depinwang/gene-expression-clustering-10sites-tpm10-separability-v1"] | EXPLORATORY deconvolution of the 10-site gene-expression signal (n=980). Cell-type marker-signature scores (7 types) per sample, then: (1) per-site composition profile, (2) composition-only site classifier, (3) expression residualized on composition then re-classified. FINDINGS: composition explains 34.7% of filtered-e... | ["10-site", "deconvolution", "microenvironment", "composition", "exploratory", "ovarian-cancer"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523287", "cluster": "ePouta", "artifact_status": "final", "canary": false, "analysis_type": "exploratory"} | 2026-06-11T09:44:28.346832+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T09:44:28.346832+00:00 |
gene-expression-clustering-10sites-deconvolution-decoupler-v1 | 13a_decoupler_prep.py + 13b_decoupler_deconv.py | decoupler 2.1.6 AUCell over PanglaoDB human markers; LogisticRegression(C=1,L2) 5-fold CV | {"composition_method": "decoupler.mt.aucell (tmin=5)", "marker_resource": "PanglaoDB via dc.op.resource (human==True), 16 TME cell types, 1712 markers", "scoring_matrix": "full 77114-symbol TPM (Ensembl->symbol, dup-symbols summed)", "residual_genes": "5000 SD genes (same as draft)", "cv": "stratified 5-fold, seed 0", ... | ["depinwang/gene-expression-clustering-10sites-deconvolution-v1"] | EXPLORATORY but STANDARD/CITABLE 10-site composition deconvolution. Replaces the homemade mean-z signature-score draft (deconvolution-v1) with decoupler AUCell (Badia-i-Mompel 2022) over 16 PanglaoDB (Franzen 2019) TME cell-type marker sets, ranking the full 77k-symbol transcriptome per sample. Same question as the dra... | ["deconvolution", "decoupler", "PanglaoDB", "AUCell", "composition", "10site", "ovarian-cancer", "gene-expression", "exploratory"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523298", "cluster": "ePouta", "artifact_status": "final", "canary": false} | 2026-06-11T11:18:13.442311+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T11:18:13.442311+00:00 |
gene-expression-clustering-10sites-splicing-separability-v1 | spl_a_prep.py + spl_b_separability.py | LogisticRegression(C=1,L2) multinomial 5-fold CV; PAM/k-medoids + average linkage | {"splicing_features": "5000 variability-filtered PSI events (NaN-free)", "expression_features": "5000 SD genes log2(TPM+1)", "clustering_input": "sqrt(JSD) matrix (981 splicing / 980 expression)", "cv": "stratified 5-fold, seed 0", "logreg_C": 1.0, "pam_restarts": 12, "min_per_class_supervised": 5} | ["depinwang/gene-expression-clustering-10sites-tpm10-separability-v1", "depinwang/gene-expression-clustering-10sites-tpm10-separability-PDS-v1"] | EXPLORATORY (no prereg) port of the PAM + supervised one-vs-rest separability probes from the expression run onto the SPLICING axis (5000 variability-filtered PSI events, NaN-free; 981 samples; splicing sqrt(JSD) matrix), so the two modalities are directly comparable (same classifier, same 5-fold CV, same metadata). KE... | ["splicing", "PSI", "separability", "PAM", "supervised", "10site", "expression-vs-splicing", "ovarian-cancer", "exploratory"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523310", "cluster": "ePouta", "artifact_status": "final", "canary": false} | 2026-06-11T11:59:20.326233+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T11:59:20.326233+00:00 |
gene-expression-clustering-10sites-pathway-enrichment-v1 | 14_enrichment.py | OLS composition-adjusted t-stat + gseapy 1.2.1 prerank (1000 perms) | {"design": "log2(TPM+1) ~ site_indicator + 16 AUCell scores", "ranking": "t-stat of site coefficient", "expressed_filter": "mean TPM>=1 (32621 genes)", "gsea": "preranked, min_size=10, max_size=500, 1000 perms, seed=0", "libraries": "MSigDB_Hallmark_2020, GO_Biological_Process_2023, Reactome_2022"} | ["depinwang/gene-expression-clustering-10sites-deconvolution-decoupler-v1"] | EXPLORATORY (no prereg) composition-adjusted pathway/GO enrichment answering: after removing generic cell-type composition, what biology still distinguishes the residual-surviving sites (LymphNode, Bowel, Tube, Ovary; the sites whose supervised separability survived composition removal in the deconvolution step)? Metho... | ["pathway-enrichment", "GSEA", "GO", "Reactome", "Hallmark", "composition-adjusted", "ovarian-cancer", "gene-expression", "exploratory"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2523313", "cluster": "ePouta", "artifact_status": "final", "canary": false} | 2026-06-11T12:25:15.000803+00:00 | null | null | null | null | null | null | -1 | 2026-06-11T12:25:15.000803+00:00 |
masld-lonp2-se-psi-nash-vs-control-psi-per-donor-v1 | analyze_lonp2se_psi.py | n/a (splicing quantification, not a model) | {"tool": "SHIBA/MameShiba v0.8.2", "minimum_reads": 10, "dedup": "UMI-deduplicated LSEC BAMs", "reference_gtf": "Ensembl-113", "event": "SE@chr16@48256610-48256741@48252365-48258618", "gene": "LONP2"} | [] | EXPLORATORY per-donor PSI for the LONP2 skipped-exon event SE@chr16@48256610-48256741@48252365-48258618 (minus strand), in liver sinusoidal endothelial cells (LSEC). Quantified with SHIBA/MameShiba v0.8.2 on UMI-deduplicated BAMs, minimum_reads=10 (donors below the read floor are NA). Two cohorts: GSE244832 (n=18 donor... | ["masld", "lonp2", "splicing", "psi", "lsec", "exploratory", "shiba"] | {"experiment_name": "masld-lonp2-se-psi-nash-vs-control", "job_id": "turso:74998090 (GSE244832) + turso:74970191 (GSE289173)", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-12T14:02:41.056881+00:00 | null | null | null | null | null | null | -1 | 2026-06-12T14:02:41.056881+00:00 |
gse190940-assay-verification-verdict-v1 | build_verdict_artifact.py | n/a (assay-identity verification from raw 10x reads) | {} | [] | Per-sample assay-identity verdict for GSE190940 (mouse visual cortex). Verifies directly from raw SRA reads whether the sample is 10x Genomics 3' single-nucleus RNA-seq. Canary on SRR17335170/GSM5754064: Claim A (10x)=PASS, Claim B (3' v3)=PASS, Claim C (single-nucleus)=INCONCLUSIVE (strongly indicated by mito~=0 + pre... | ["gse190940", "assay-verification", "10x-genomics", "single-nucleus", "canary"] | {"experiment_name": "gse190940-assay-verification", "cluster": "turso", "artifact_status": "final", "canary": true} | 2026-06-12T15:22:04.129942+00:00 | null | null | null | null | null | null | -1 | 2026-06-12T15:17:13.293316+00:00 |
jinyang-majiq-psi-s1-v1 | work/jinyang-majiq-psi/s1/run_s1.sh | MAJIQ v2.5.11 (deltapsi) | {"changing_threshold": 0.2, "group_sizes": {"HFD": 3, "ND": 3}, "comparison": "HFD vs ND (individual-level, 3v3)", "annotation": "GENCODE vM20 basic"} | [] | MAJIQ deltapsi S1 — HFD vs ND 3v3 individual-level differential splicing on mouse single-cell pseudo-bulk (GENCODE vM20). 1488 LSVs; 470 with P(|ΔPSI|≥0.2)≥0.90, 339 ≥0.95. Bayesian posterior probabilities (no p-values). Biological hits include Mbnl2 (canonical splicing regulator). | ["jinyang-majiq-psi", "splicing", "majiq", "deltapsi", "HFD-vs-ND"] | {"experiment_name": "jinyang-majiq-psi", "job_id": "turso:74874734", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-12T19:28:14.012732+00:00 | null | null | null | null | null | null | -1 | 2026-06-12T19:28:14.012732+00:00 |
jinyang-gse319320-rmats-psi-matrix-jc-v1 | build_psi_matrix_319320.py | N/A (alternative-splicing quantification) | {"tool": "rMATS-turbo v4.3.0", "counting_method": "JC (junction count)", "readLength": 132, "variable_read_length": true, "anchorLength": 1, "allow_clipping": true, "task": "both", "aligner": "STAR 2.7.11b 2-pass", "reference": "GRCh38 Ensembl release-113", "psi": "rMATS IncLevel, per replicate, not rounded"} | ["depinwang/jinyang-gse319320-rmats-psi-ko-vs-control-v1"] | GSE319320 per-sample PSI matrix: 147,444 rMATS-turbo JC events x 12 samples (6 ADAR1-KO + 6 control human macrophages). Per-replicate PSI from a single 6v6 rMATS run (no event merging). Column-to-group mapping validated: mean(per-sample PSI) == reported group PSI at 100%. | ["jinyang-gse319320-rmats-psi", "splicing", "rmats", "psi-matrix", "ADAR1", "macrophage", "GRCh38"] | {"experiment_name": "jinyang-gse319320-rmats-psi", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-14T16:46:23.136678+00:00 | null | null | null | null | null | null | -1 | 2026-06-14T16:38:59.395606+00:00 |
jinyang-gse307402-rmats-psi-matrix-jc-v1 | build_psi_matrix_307402.py | N/A (alternative-splicing quantification) | {"tool": "rMATS-turbo v4.3.0", "counting_method": "JC (junction count)", "readLength": 132, "variable_read_length": true, "anchorLength": 1, "allow_clipping": true, "task": "both", "aligner": "STAR 2.7.11b 2-pass", "reference": "GRCh38 Ensembl release-113", "psi": "rMATS IncLevel, per replicate, not rounded", "merge_ke... | ["depinwang/jinyang-gse307402-rmats-psi-siadar1-vs-control-v1", "depinwang/jinyang-gse307402-rmats-psi-p150-vs-control-v1"] | GSE307402 unified per-sample PSI matrix: 171,526 rMATS-turbo JC events x 15 samples (5 control + 5 siADAR1 both-isoform + 5 siADAR1-p150 human macrophages). Merged from the two original rMATS runs (A: siADAR1 vs ctrl; B: p150 vs ctrl) by FULL event-coordinate key. 128,600 events detected in both runs (all 15 samples); ... | ["jinyang-gse307402-rmats-psi", "splicing", "rmats", "psi-matrix", "ADAR1", "p150", "macrophage", "GRCh38"] | {"experiment_name": "jinyang-gse307402-rmats-psi", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-14T16:46:42.316430+00:00 | null | null | null | null | null | null | -1 | 2026-06-14T16:39:39.295277+00:00 |
jinyang-gse307402-majiq-psi-canary-v1 | run_canary.sh | N/A (MAJIQ LSV quantification) | {"tool": "MAJIQ v2.5.11 deltapsi", "modules": "build->deltapsi->voila tsv", "strandness": "reverse (fr-firststrand, ReadsPerGene-verified)", "genome": "GRCh38 Ensembl-113", "threshold": 0.2, "min_experiments": 0.5, "min_reads": 5, "design": "CANARY 2v2 (not the full 5v5/6v6)"} | [] | GSE307402 MAJIQ deltapsi CANARY (2v2): 597 LSVs for A (siADAR1 vs ctrl) + 627 for B (p150 vs ctrl). Validates the human MAJIQ pipeline end-to-end before the full 5v5 run. All red-team gates passed (GFF3 gene-count parity 78724, strand=reverse effective, silent-zero guard, PSI in [0,1]). | ["jinyang-gse307402-majiq-psi", "majiq", "lsv", "splicing", "canary", "ADAR1", "p150", "GRCh38"] | {"experiment_name": "jinyang-gse307402-majiq-psi", "job_id": "turso:75005890", "cluster": "turso", "artifact_status": "partial", "canary": true} | 2026-06-15T07:29:48.320101+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T07:29:48.320101+00:00 |
jinyang-gse319320-majiq-psi-canary-v1 | run_canary.sh | N/A (MAJIQ LSV quantification) | {"tool": "MAJIQ v2.5.11 deltapsi", "modules": "build->deltapsi->voila tsv", "strandness": "reverse (fr-firststrand, ReadsPerGene-verified)", "genome": "GRCh38 Ensembl-113", "threshold": 0.2, "min_experiments": 0.5, "min_reads": 5, "design": "CANARY 2v2 (not the full 5v5/6v6)"} | [] | GSE319320 MAJIQ deltapsi CANARY (2v2): 849 LSVs for ADAR1-KO vs control. Validates the human MAJIQ pipeline end-to-end before the full 6v6 run. All red-team gates passed. | ["jinyang-gse319320-majiq-psi", "majiq", "lsv", "splicing", "canary", "ADAR1", "knockout", "GRCh38"] | {"experiment_name": "jinyang-gse319320-majiq-psi", "job_id": "turso:75005891", "cluster": "turso", "artifact_status": "partial", "canary": true} | 2026-06-15T07:30:02.268266+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T07:30:02.268266+00:00 |
masld-lonp2-exon3-psi-feasibility-per-sample-table-v1 | 01_persample.py + 02_build_table.py | N/A — junction-counting / coverage pipeline (no ML model) | {} | [] | Per-sample LONP2 exon-3 (cassette SE) feasibility table in LSEC pseudobulk. Junction-based PSI (rMATS SE logic) + two normalized-depth axes + two feasibility gates. effective N per chemistry (NOT pooled). Descriptive/QC; exon 3 = seen event A. | ["masld", "lonp2", "alternative-splicing", "lsec", "feasibility"] | {"experiment_name": "masld-lonp2-exon3-psi-feasibility", "artifact_status": "final", "cluster": "turso"} | 2026-06-15T09:31:22.156250+00:00 | masld-lonp2-exon3-psi-feasibility | null | eval_result | table | null | null | -1 | 2026-06-15T07:32:06.580585+00:00 |
masld-lonp2-exon3-psi-feasibility-junction-count-matrix-v1 | 01_persample.py + 02_build_table.py | N/A — junction-counting pipeline (no ML model) | {} | [] | LONP2 junction-count matrix (87 junctions x 35 LSEC-pseudobulk samples), the VariancePartition input. Rows = introns by exact 1-based coords; is_target marks IJ1/IJ2/SJ. Counts are spanning-read counts (min_anchor=1, dups kept since BAMs are UMI/Read-deduped upstream). Cross-chemistry: chemistry explains 68.6% of IJ2 v... | ["masld", "lonp2", "alternative-splicing", "lsec", "variancepartition"] | {"experiment_name": "masld-lonp2-exon3-psi-feasibility", "artifact_status": "final", "cluster": "turso"} | 2026-06-15T09:31:32.085610+00:00 | masld-lonp2-exon3-psi-feasibility | null | processed_data | table | null | null | -1 | 2026-06-15T07:58:09.364495+00:00 |
masld-lonp2-exon3-psi-feasibility-coverage-figures-v1 | 03_coverage_profile.sh + 03b_overlay_profile.py + 04_variance_partition.R | N/A — deeptools coverage / VariancePartition figures (no ML model) | {} | [] | Renderable coverage + VariancePartition figures for LONP2 exon-3 LSEC feasibility. Combined overlays are the CORRECTED versions (deeptools 'bins'-row parser bug fixed). Descriptive/QC — no disease claim. | ["masld", "lonp2", "lsec", "coverage", "image"] | {"experiment_name": "masld-lonp2-exon3-psi-feasibility", "artifact_status": "final", "cluster": "turso"} | 2026-06-15T09:31:42.898027+00:00 | masld-lonp2-exon3-psi-feasibility | null | processed_data | image | null | null | -1 | 2026-06-15T08:15:02.489945+00:00 |
jinyang-gse307402-majiq-psi-deltapsi-A-v1 | upload_full.py | MAJIQ-v2.5.11 | {} | [] | MAJIQ deltapsi: siADAR1 knockdown vs control in GSE307402 human macrophages. 5v5, GRCh38 Ensembl-113, strandness=reverse. | ["majiq", "deltapsi", "splicing", "jinyang-gse307402-majiq-psi", "adar1", "human", "full-run"] | {"experiment_name": "jinyang-gse307402-majiq-psi", "job_id": "turso:75007156", "cluster": "turso", "artifact_status": "final", "canary": false, "comparison": "siADAR1 vs control (5v5)", "tool": "MAJIQ v2.5.11", "genome": "GRCh38 Ensembl-113", "strandness": "reverse (fr-firststrand)", "changing_threshold": 0.2, "group_s... | 2026-06-15T09:55:21.790795+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T09:55:21.790795+00:00 |
jinyang-gse307402-majiq-psi-deltapsi-B-v1 | upload_full.py | MAJIQ-v2.5.11 | {} | [] | MAJIQ deltapsi: p150 isoform knockdown vs control in GSE307402 human macrophages. 5v5, GRCh38 Ensembl-113, strandness=reverse. | ["majiq", "deltapsi", "splicing", "jinyang-gse307402-majiq-psi", "adar1", "human", "full-run"] | {"experiment_name": "jinyang-gse307402-majiq-psi", "job_id": "turso:75007156", "cluster": "turso", "artifact_status": "final", "canary": false, "comparison": "p150 vs control (5v5)", "tool": "MAJIQ v2.5.11", "genome": "GRCh38 Ensembl-113", "strandness": "reverse (fr-firststrand)", "changing_threshold": 0.2, "group_size... | 2026-06-15T09:55:38.088077+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T09:55:38.088077+00:00 |
jinyang-gse319320-majiq-psi-deltapsi-v1 | upload_full.py | MAJIQ-v2.5.11 | {} | [] | MAJIQ deltapsi: ADAR1 knockout vs control in GSE319320 human macrophages. 6v6, GRCh38 Ensembl-113, strandness=reverse. | ["majiq", "deltapsi", "splicing", "jinyang-gse319320-majiq-psi", "adar1", "human", "full-run"] | {"experiment_name": "jinyang-gse319320-majiq-psi", "job_id": "turso:75007157", "cluster": "turso", "artifact_status": "final", "canary": false, "comparison": "ADAR1-KO vs control (6v6)", "tool": "MAJIQ v2.5.11", "genome": "GRCh38 Ensembl-113", "strandness": "reverse (fr-firststrand)", "changing_threshold": 0.2, "group_... | 2026-06-15T09:55:56.513462+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T09:55:56.513462+00:00 |
jinyang-gse307402-shiba-psi-canary-v1 | upload_canary.py | Shiba-v0.8.2 | {} | [] | Shiba v0.8.2 (MameShiba) canary PSI matrix — GSE307402, 4 samples (2 ctrl + 2 siADAR1), GRCh38 Ensembl-113, strand=XS. only_psi=True. | ["shiba", "psi-matrix", "canary", "jinyang-gse307402-shiba-psi", "human", "adar1"] | {"experiment_name": "jinyang-gse307402-shiba-psi", "job_id": "turso:75007457", "cluster": "turso", "artifact_status": "canary", "canary": true, "tool": "Shiba v0.8.2 (MameShiba)", "mode": "only_psi=True", "genome": "GRCh38 Ensembl-113", "strand": "XS (STAR intronMotif XS tags)", "n_samples": 4, "minimum_reads": 10, "ev... | 2026-06-15T11:07:59.315660+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T11:07:59.315660+00:00 |
jinyang-gse319320-shiba-psi-canary-v1 | upload_canary.py | Shiba-v0.8.2 | {} | [] | Shiba v0.8.2 (MameShiba) canary PSI matrix — GSE319320, 4 samples (2 ctrl + 2 ADAR1-KO), GRCh38 Ensembl-113, strand=XS. only_psi=True. | ["shiba", "psi-matrix", "canary", "jinyang-gse319320-shiba-psi", "human", "adar1"] | {"experiment_name": "jinyang-gse319320-shiba-psi", "job_id": "turso:75007459", "cluster": "turso", "artifact_status": "canary", "canary": true, "tool": "Shiba v0.8.2 (MameShiba)", "mode": "only_psi=True", "genome": "GRCh38 Ensembl-113", "strand": "XS (STAR intronMotif XS tags)", "n_samples": 4, "minimum_reads": 10, "ev... | 2026-06-15T11:08:27.934726+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T11:08:27.934726+00:00 |
jinyang-gse319320-shiba-psi-full-v1 | upload_gse319320_full.py | Shiba-v0.8.2 | {} | [] | Shiba v0.8.2 (MameShiba) FULL-RUN PSI matrix — GSE319320 hMDM ADAR1-KO. 12 samples (6 ctrl + 6 KO), 324,343 events, 8 event types. Strand=XS (STAR intronMotif), only_psi=True, minimum_reads=10. Completed in 2h7m. Job turso:75007578. | ["shiba", "psi-matrix", "gse319320", "adar1-ko", "human-mdm", "splicing", "full-run", "final"] | {"experiment_name": "jinyang-gse319320-shiba-psi", "job_id": "turso:75007578", "cluster": "turso", "artifact_status": "final", "canary": false, "tool": "Shiba v0.8.2 (MameShiba)", "mode": "only_psi=True, --mame (steps 1-4 only)", "genome": "GRCh38 Ensembl-113", "strand": "XS (STAR intronMotif XS tags)", "n_samples": 12... | 2026-06-15T13:14:58.668039+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T13:14:58.668039+00:00 |
jinyang-gse307402-shiba-psi-full-v1 | upload_gse307402_full.py | Shiba-v0.8.2 | {} | [] | Shiba v0.8.2 (MameShiba) FULL-RUN PSI matrix — GSE307402 hMDM siADAR1/p150 KD. 15 samples (5 ctrl + 5 siADAR1 + 5 p150), 342,183 events, 8 event types. Strand=XS (STAR intronMotif), only_psi=True, minimum_reads=10. Completed in 2h35m. Job turso:75007577. | ["shiba", "psi-matrix", "gse307402", "adar1", "siadar1", "p150", "human-mdm", "splicing", "full-run", "final"] | {"experiment_name": "jinyang-gse307402-shiba-psi", "job_id": "turso:75007577", "cluster": "turso", "artifact_status": "final", "canary": false, "tool": "Shiba v0.8.2 (MameShiba)", "mode": "only_psi=True, --mame (steps 1-4 only)", "genome": "GRCh38 Ensembl-113", "strand": "XS (STAR intronMotif XS tags)", "n_samples": 15... | 2026-06-15T13:44:05.894475+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T13:44:05.894475+00:00 |
masld-gse244832-lsec-pseudobulk-fastq-manifest-v1 | bam_to_fastq.sbatch | N/A — samtools fastq BAM->FASTQ format conversion (no model) | {} | ["depinwang/masld-gse244832-lsec-bam-dedup-stats"] | Per-patient FASTQ census for GSE244832 LSEC pseudobulk FASTQs (single-end cDNA, from UMI-deduplicated dedup BAMs). One row per patient: BAM-vs-FASTQ read counts, lossless match, read-length median (cDNA check), bytes, md5, flag. | ["masld", "gse244832", "lsec", "pseudobulk", "fastq", "bam2fastq", "rna-editing"] | {"experiment_name": "masld-gse244832-lsec-pseudobulk-fastq", "job_id": "kale:75008393", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-15T15:22:43.263691+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T15:22:43.263691+00:00 |
masld-gse289173-lsec-pseudobulk-fastq-manifest-v1 | bam_to_fastq.sbatch | N/A — samtools fastq BAM->FASTQ format conversion (no model) | {} | ["depinwang/masld-gse289173-lsec-bam-dedup-stats-v1"] | Per-donor (GSM) FASTQ census for GSE289173 LSEC pseudobulk FASTQs (single-end cDNA, from UMI-deduplicated dedup BAMs). One row per donor: BAM-vs-FASTQ read counts, lossless match, read-length median (cDNA check), bytes, md5, flag. | ["masld", "gse289173", "lsec", "pseudobulk", "fastq", "bam2fastq", "rna-editing"] | {"experiment_name": "masld-gse289173-lsec-pseudobulk-fastq", "job_id": "kale:75008571", "cluster": "kale", "artifact_status": "final", "canary": false} | 2026-06-15T17:29:48.902458+00:00 | null | null | null | null | null | null | -1 | 2026-06-15T17:29:48.902458+00:00 |
masld-gse289173-lsec-bcsplit-canary-compare-v1 | split_by_barcode.sbatch + upload_compare.py | N/A — TSRdetector-style barcode FASTQ split vs BAM-derived (no model) | {"chemistry": "SC3Pv3", "r1rt_start": 28, "cb_len": 16, "umi_len": 12} | ["masld-gse289173-lsec-pseudobulk-fastq-manifest-v1", "masld-gse289173-lsec-bam-dedup-stats-v1"] | Canary comparison (donor GSM8785694) of a TSRdetector-style raw barcode/cell-type FASTQ split (cluster_fastq_np_PE_files.cpp, adapted for RNA editing: real base quality preserved, CB+UMI carried in read names, chemistry-correct R1[28:] read-through) vs the previously produced BAM-derived single-end cDNA FASTQ. Raw barc... | ["masld", "gse289173", "lsec", "fastq", "rna-editing", "tsrdetector", "barcode-split", "canary"] | {"experiment_name": "masld-gse289173-lsec-bcsplit-fastq", "job_id": "kale:75013520", "cluster": "kale", "artifact_status": "partial", "canary": true} | 2026-06-16T08:33:20.960321+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T08:33:20.960321+00:00 |
gene-expression-clustering-10sites-ovary-asc-2site-within-pds-v1 | 11_within_pds_control.py + 13_within_pds_clean_features.py | PAM/k-medoids k=2; kNN(k=15, precomputed JSD); LogisticRegression(C=1,L2) w/ in-fold feature selection | {"sample_subset": "PDS-only, n=270 (Ovary 161, Ascites 109)", "gene_sweep": [1000, 2000, 5000, 10000], "cv": "stratified 5-fold, seed 0", "distance": "sqrt(JSD/ln2) on L1-normalized log2(TPM+1)", "pam_restarts": 12, "feature_selection": "top-SD; clean=re-selected within PDS / inside CV fold"} | ["depinwang/gene-expression-clustering-10sites-ovary-asc-2site-v1", "depinwang/gene-expression-clustering-10sites-ovary-asc-2site-separability-v1"] | CONTROLS for the Ovary(solid)-vs-Ascites(liquid) separability follow-up: does the separation survive holding TREATMENT PHASE constant, and is it robust to FEATURE SELECTION? The site x phase mix is imbalanced (Ovary: 0 Recurrence; Ascites: 47 Recurrence), and full-set PERMANOVA R2_phase=0.050 ~ R2_site=0.096, so phase ... | ["ovary-vs-asc-2site", "within-pds", "phase-control", "feature-selection", "robustness", "follow-up", "ovarian-cancer", "gene-expression"] | {"experiment_name": "gene-expression-clustering-10sites", "job_id": "ePouta:2524661", "cluster": "ePouta", "artifact_status": "final", "canary": false, "prereg_commit": "d35590a + d40c665"} | 2026-06-16T08:50:22.804450+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T08:50:22.804450+00:00 |
fastq-lane-count-audit-per-sample-v1 | 01_count_lanes_from_manifests.py | n/a (metadata parsing, no model) | {"lane_token_regex": "_L(\\d{1,3})_", "flowcell_lane_regex": "([A-Za-z0-9]+)_L(\\d{1,3})_", "source_dir": "/home/arkku/group/sysimeta/depin/Project/20240730_Ovarian_cancer_project/test"} | [] | Per-sample sequencing-lane count for 1076 original ovarian-cancer RNA-seq samples across 10 anatomical sites. Phase 1 (metadata-only): derived from the pre-merge *_all_samples_fastq_paths.csv manifests on ePouta. Two independent estimates (NumPairs vs distinct flowcell-lane parsed from filenames) agree on all 1070 dete... | ["fastq", "lanes", "qc", "ovarian-cancer", "rna-seq", "inventory"] | {"experiment_name": "fastq-lane-count-audit", "cluster": "ePouta (source manifests)", "artifact_status": "final", "canary": false} | 2026-06-16T09:03:35.265327+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T09:03:35.265327+00:00 |
masld-gse289173-lsec-unaligned-recovery-canary-v1 | recover.sbatch + upload_yield.py | N/A — STAR re-alignment + umi_tools dedup of cellranger-unmapped reads (no model) | {"aligner": "STAR-2.7.11b", "outFilterMatchNmin": 30, "outFilterMismatchNoverLmax": 0.1, "outFilterMatchNminOverLread": 0} | ["masld-gse289173-lsec-pseudobulk-fastq-manifest-v1"] | Canary (GSM8785694) for recovering cellranger-UNMAPPED LSEC reads as additional RNA-editing coverage. 222,550 unmapped LSEC reads re-aligned with STAR-2.7.11b (permissive: soft-clip, >=30 genomic bp, <=10% mismatch) -> 81,620 uniquely mapped (36.7%) -> 70,284 UMI-deduped -> 60,172 GENIC. That is +4.06% genic deduped co... | ["masld", "gse289173", "lsec", "rna-editing", "unaligned-recovery", "star", "canary"] | {"experiment_name": "masld-gse289173-lsec-unaligned-recovery", "job_id": "kale:75014075", "cluster": "kale", "artifact_status": "partial", "canary": true} | 2026-06-16T09:24:41.699615+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T09:24:41.699615+00:00 |
fastq-lane-count-audit-phase2-header-lanes-v1 | phase2_header_lane_check.py | n/a (FASTQ header parsing, no model) | {"n_reads_per_file": 500, "header_parser": "3-family: casava18 (4th colon field), illumina_old (2nd colon field), bgi_mgi (L<n> in read name)"} | ["depinwang/fastq-lane-count-audit-per-sample-v1"] | Phase 2 ground truth: read the first 500 read headers of every R1 FASTQ (1413 files, 1070 non-empty samples, 10 sites) on ePouta and parse the (flowcell, lane) encoded in the header, then cross-check vs the Phase-1 filename-derived lane counts. Result: 930/930 token files match header lane exactly, 483 no-token files r... | ["fastq", "lanes", "qc", "ovarian-cancer", "rna-seq", "ground-truth", "read-headers"] | {"experiment_name": "fastq-lane-count-audit", "job_id": "ePouta:2524670", "cluster": "ePouta", "artifact_status": "final", "canary": false} | 2026-06-16T09:36:39.892630+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T09:36:39.892630+00:00 |
star-alignment-qc-per-sample-v1 | 01_parse_star_logs.py | n/a (STAR log parsing) | {} | [] | Per-sample STAR 2nd-pass alignment metrics for 1048 aligned ovarian-cancer RNA-seq samples (10 sites), parsed from Log.final.out. Uniq-mapped median 89.2%, total mapped median 96.4%, mismatch/base max 0.63%; 31 samples uniq<70% (high multi-mapping). | ["star", "alignment", "qc", "rna-seq", "ovarian-cancer"] | {"experiment_name": "star-alignment-qc", "cluster": "ePouta", "artifact_status": "final", "canary": false} | 2026-06-16T13:06:45.766502+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T13:06:45.766502+00:00 |
masld-gse289173-r1tail-cdna-feasibility-canary-v1 | r1tail_feasibility.sbatch + upload_feasibility.py | N/A — STAR-2.7.11b alignment + umi_tools dedup of raw R1 tails (no model) | {"aligner": "STAR-2.7.11b", "clip5p": 28, "outFilterMatchNmin": 20, "outFilterMismatchNoverLmax": 0.1, "subsample_reads": 3000000, "pas_window_bp": 100, "r2_subsample": 0.02} | [] | Feasibility canary (GSM8785694, ~3M reads): can GSE289173 R1 carry mappable, 3'-biased near-PAS cDNA usable for scTail-style APA? Raw R1 seq[28:] (clip 28 not scTail's 60, since our tail has NO polyT), TSO-led dropped (23.8%), STAR permissive align -> 23.6% uniquely mapped (68.8% multimap, tail=41bp too short), 95.8% g... | ["masld", "gse289173", "r1-tail", "scTail", "apa", "pas", "feasibility", "canary", "no-go"] | {"experiment_name": "masld-gse289173-r1tail-cdna-feasibility", "job_id": "kale:75019439", "cluster": "kale", "artifact_status": "final", "canary": true} | 2026-06-16T13:06:58.282950+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T13:06:58.282950+00:00 |
masld-gse289173-r1tail-editing-spectrum-canary-v1 | spectrum.py + spectrum.sbatch + upload_spectrum.py | N/A — pysam base-substitution spectrum of deduped BAMs (no model, no alignment) | {"base_quality_min": 30, "floor": "8 transversions", "primary_metric": "editing_specificity_AGTC_over_CTGA", "gate": "specificity>1.2 AND editing_rate_ratio>=0.6"} | [] | RNA-editing feasibility canary (GSM8785694): base-substitution spectrum of R1-tail cDNA vs R2, to decide if R1 carries real A-to-I editing signal or just error. Per reference-base-opportunity rates, BASEQ>=30, floor = 8 transversions (C>T/G>A kept separate as deamination). RESULT: R1 editing_specificity (A>G+T>C)/(C>T+... | ["masld", "gse289173", "r1-tail", "rna-editing", "substitution-spectrum", "ADAR", "canary"] | {"experiment_name": "masld-gse289173-r1tail-editing-feasibility", "job_id": "kale:75019961", "cluster": "kale", "artifact_status": "final", "canary": true} | 2026-06-16T14:31:29.845944+00:00 | null | null | null | null | null | null | -1 | 2026-06-16T14:31:29.845944+00:00 |
splicing-ovary-vs-asc-2site-results-v1 | pipeline/03_compute_jsd.py + 04_separation_metrics.py | n/a (statistical pipeline: Bernoulli sqrt-JSD + PERMANOVA) | {"distance": "bernoulli_per_event_sqrt_jsd", "n_features": 5000, "feature_selection": "top_variance_within_subset, drop_any_nan", "permanova_B": 9999, "seed": 0, "clustering": "average_linkage_k2"} | [] | PSI vs TPM, Ovary-vs-Ascites (same 364 samples, same pipeline). UNSUPERVISED: both ARI~0 by average linkage (degenerate 363-vs-1 split) and R2_site PSI 0.066 < TPM 0.096. BUT the proper reads OVERTURN 'unclusterable': PAM ARI PSI 0.75 / TPM 0.65 (LINKAGE ARTIFACT), and supervised within-NovaSeq AUC PSI 0.94 / TPM 0.98 ... | ["splicing", "psi", "ovary", "ascites", "jsd", "separability", "modality-comparison"] | {"experiment_name": "splicing-ovary-vs-asc-2site", "cluster": "local (macOS)", "artifact_status": "final", "canary": false} | 2026-06-18T08:58:27.882531+00:00 | null | null | null | null | null | null | -1 | 2026-06-18T08:40:48.762251+00:00 |
jinyang-quantas-psi-shiba-concordance-v1 | concordance_with_shiba/scripts/06_compare.py | n/a (splicing-tool concordance, no model) | {"cell_threshold_abs_delta": 0.1, "event_min_concordant_bulks": 4, "verdict_agree_min_events": 6, "n_events": 8, "pooling": "strategy1_6_pseudobulks"} | ["depinwang/jinyang-quantas-psi-s1-cass-v1", "depinwang/jinyang-splicing-psi-strategy1-v1"] | Per-(event x pseudo-bulk) Shiba(SE) vs Quantas(cass) cassette PSI concordance for 8 high-coverage cassette exons on the shared HFD-vs-ND Strategy-1 pseudo-bulks. Verdict: tools AGREE 8/8 events concordant; global signed median delta (Quantas-Shiba)=0.0000. Pre-registered (commit 84196f0); matching by single-cassette ge... | ["jinyang-quantas-psi", "concordance", "shiba-vs-quantas", "cassette-psi", "methods-validation"] | {"experiment_name": "jinyang-quantas-psi", "artifact_status": "final", "canary": false} | 2026-06-22T14:34:25.765750+00:00 | null | null | null | null | null | null | -1 | 2026-06-22T14:34:25.765750+00:00 |
scses-fig2a-repro-canary-imputed-psi-v1 | run_scses_steps.R | SCSES 1.0.0 (pre-trained Estimation model + TF autoencoder) | {"event_type": "SE;RI;A3SS;A5SS;MXE", "cell_similarity_data": "EXP_RBP", "feature_num": 1000, "AE_epoch": 100, "AE_embedding": 32, "AE_layer": "[256,128]", "KNN_cell_kmax": 8, "KNN_cell_kmin": 3, "KNN_event_k": 5, "genome": "hg19 (demo subset)"} | [] | CANARY artifact for SCSES Fig 2a reproduction on puhti. Imputed single-cell PSI matrix (788 events x 15 cells) from the SCSES 15-cell hg19 cell_line demo, produced by the full Step1-8 pipeline (gene expr via featureCounts -> detectEvents MAJIQ+IRFinder+rMATS -> getRawRC/PSI -> cell+event similarity (EXP_RBP, 134 RBPs) ... | ["scses-fig2a-repro", "canary", "single-cell-splicing", "psi-imputation", "scses"] | {"experiment_name": "scses-fig2a-repro", "job_id": "puhti:35263432", "cluster": "puhti", "artifact_status": "final", "canary": true} | 2026-06-24T21:11:29.631375+00:00 | null | null | null | null | null | null | -1 | 2026-06-24T21:11:29.631375+00:00 |
rmats-turbo-psi-1048-canary-v1 | pipeline/04_prep.sbatch + 06_post.sbatch + 08_validate.py | rMATS-turbo v4.3.0 (splicing quantification, not a model) | {"libType": "fr-firststrand (all 3 platforms, RSeQC-confirmed)", "readLength": "150 + --variable-read-length", "task": "prep+post single-group --statoff (quantification only)", "novelSS": false, "allow_clipping": false, "t": "paired", "gtf": "Ensembl 113 homo_sapiens"} | [] | CANARY per-sample PSI matrices from rMATS-turbo single-group --statoff quantification (no grouping, no differential test), validating the rmats-turbo-psi-1048 pipeline E2E before the full 1048-BAM run.
The default loadable config is **SE_JCEC** (skipped-exon, junction+exon reads): 155,399 events x 7 samples. ALL 10 ma... | ["rmats-turbo-psi-1048", "canary", "psi", "splicing", "rmats-turbo"] | {"experiment_name": "rmats-turbo-psi-1048", "job_id": "ePouta:2533258(prep)/2533437(post)/2533465(validate)", "cluster": "ePouta", "artifact_status": "final", "canary": true} | 2026-06-26T12:35:49.689725+00:00 | null | null | null | null | null | null | -1 | 2026-06-26T12:35:49.689725+00:00 |
jinyang-gse319320-shiba-psi-tpm-v1 | run_expression.sh + Shiba src/expression.py | n/a (gene-level expression quantification) | {"quantifier": "featureCounts (subread, via Shiba v0.8.2)", "feature_type": "exon", "group_by": "gene_id", "paired_end": true, "strandedness": "unstranded (-s 0; Shiba default) \u2014 library is reverse-stranded", "gtf": "Ensembl release 113 (homo_sapiens), 78,724 genes", "bams": "STAR 2-pass Basic, GRCh38 Ensembl-113 ... | [] | Gene-level TPM matrix for GSE319320: 12 human monocyte-derived-macrophage bulk paired-end RNA-seq samples, 6 ADAR1-KO (CRISPR) vs 6 non-targeting control. Produced by the Shiba v0.8.2 expression module (featureCounts -t exon -g gene_id, paired-end, unstranded by Shiba's default; -s NOT set even though the library is re... | ["jinyang-gse319320-shiba-psi", "tpm", "gene-expression", "GSE319320", "ADAR1", "human-macrophage", "ensembl-113", "shiba"] | {"tool": "Shiba v0.8.2 src/expression.py: featureCounts (paired-end, UNSTRANDED per Shiba default) -> TPM", "experiment_name": "jinyang-gse319320-shiba-psi", "job_id": "turso:75057604", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-28T14:40:46.598637+00:00 | null | null | null | null | null | null | -1 | 2026-06-28T14:40:46.598637+00:00 |
jinyang-gse307402-shiba-psi-tpm-v1 | run_tpm.sh + expression.py (Shiba v0.8.2 Step 5) | N/A (gene expression quantification, not a model) | {"tool": "Shiba v0.8.2 expression.py (featureCounts + TPM)", "featureCounts": "-t exon -g gene_id (unstranded), paired-end auto-detected", "gtf": "Homo_sapiens Ensembl-113", "n_samples": 15, "n_genes": 78724} | [] | Gene-level TPM expression matrix for GSE307402 (15 hMDM samples: 5 control, 5 siADAR1, 5 p150) produced by Shiba v0.8.2's expression step (featureCounts -> TPM). gene_name column added from Ensembl-113 GTF. Companion to the Shiba PSI matrix; shares the same 15 STAR BAMs as the rMATS/MAJIQ siblings. NOTE: featureCounts ... | ["jinyang-gse307402-shiba-psi", "TPM", "expression", "GSE307402", "shiba"] | {"experiment_name": "jinyang-gse307402-shiba-psi", "job_id": "turso:75057608", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-06-28T15:12:02.820934+00:00 | null | null | null | null | null | null | -1 | 2026-06-28T14:43:34.557212+00:00 |
scses-fig2a-repro-canary-hg38-imputed-psi-v1 | run_scses_steps.R (driver) + run_resume_hg38.sbatch (resume of run_canary_hg38.sbatch) | SCSES pre-trained imputation (Step7 Estimation, model_change_*.rdata; hg19/hg38 shared) | {"genome": "hg38 / GRCh38 Ensembl release 115, Option B (chr-prefixed relabel)", "n_cells": 10, "n_events": 26330, "event_type": "SE;RI;A3SS;A5SS;MXE", "imputation": "SCSES pre-trained (kcell_min=3, kcell_max=8)", "aligner": "STAR 2.7.11b (pybio), paired-end", "psi_estimator": "SCSES Step7 Estimation (pre-trained)"} | [] | Stage-0 hg38 canary — SCSES Step1-8 end-to-end on 10 cells with Option-B chr-prefixed GRCh38 (Ensembl release 115 relabeled chr1..chrMT). Validates the full multi-language stack (R + Python/TensorFlow + MATLAB-MCR + MAJIQ/IRFinder/rMATS/STAR) on hg38. Imputed PSI matrix 26330 events x 10 cells; NA=0; range [0,1]; mean ... | ["scses-fig2a-repro", "canary", "hg38", "imputed-psi", "splicing"] | {"experiment_name": "scses-fig2a-repro", "job_id": "puhti:35320394 (resume of puhti:35305040)", "cluster": "puhti", "artifact_status": "final", "canary": true} | 2026-06-29T17:59:04.938137+00:00 | null | null | null | null | null | null | -1 | 2026-06-29T17:59:04.938137+00:00 |
scses-tissue-survivorship-canary-lr-ref-se-v1 | pipeline/stage_a_count.py + stage_a_reference.sh (SiCeLoRe 2.1) | SiCeLoRe-2.1 + minimap2-2.17 (no ML model) | {"delta_bp": 5, "lr_reads_subset": 3000000, "sr_cells": 1122, "event_universe": "fig2a run_hg38 SE.txt (33679 SE)", "n_LR_strata": "[3,5)[5,10)[10,20)[20,inf)", "psi_orientation": "inclusion/(inclusion+exclusion) -- matches SCSES rc_to_psi"} | [] | CANARY plumbing artifact. Per-(cell, SE-event) long-read PSI reference from SiCeLoRe consensus molecules over the SCSES SE event universe. Built from a 3M-read ONT subset (cancer LR) + 1122 STARsolo-filtered cells; events = fig2a run_hg38 SE.txt (33679 SE). Validates the novel 3-way molecule counter (inclusion/exclusio... | ["scses-tissue-survivorship", "canary", "long-read", "splicing", "psi", "reference", "SE"] | {"experiment_name": "scses-tissue-survivorship", "job_id": "puhti:35331987(SiCeLoRe)+35332877(count)", "cluster": "puhti", "artifact_status": "partial", "canary": true} | 2026-06-30T21:18:01.905072+00:00 | null | null | null | null | null | null | -1 | 2026-06-30T21:18:01.905072+00:00 |
scses-fig2a-repro-stage1-hcc1954-imputed-psi-v1 | run_line_scses.sbatch (LINE=HCC1954) + run_scses_steps.R | SCSES pre-trained imputation (Step7 Estimation, model_change_*.rdata) | {"cell_line": "HCC1954", "source": "SRP041736 (Pollen 2014, full-length Smart-seq2)", "genome": "hg38 GRCh38 Ensembl release 115, Option B (chr-prefixed)", "n_cells": 44, "n_events": 34203, "event_type": "SE;RI;A3SS;A5SS;MXE", "imputation": "SCSES pre-trained (kcell_min=3, kcell_max=8)", "aligner": "STAR 2.7.11b shared... | [] | Stage-1 per-line canary — SCSES Step1-8 end-to-end on ALL 44 HCC1954 single cells (SRP041736, hg38 Option-B chr-prefixed GRCh38). First real Fig-2a-line SCSES run, validating the per-line architecture at scale. Imputed PSI 34203 events x 44 cells; NA=0; range [0,1]; mean 0.729 sd 0.349; all 5 event types (SE=29223/MXE=... | ["scses-fig2a-repro", "stage1", "canary", "hg38", "HCC1954", "imputed-psi", "splicing"] | {"experiment_name": "scses-fig2a-repro", "job_id": "puhti:35329793", "cluster": "puhti", "artifact_status": "final", "canary": true} | 2026-07-01T11:29:45.298029+00:00 | null | null | null | null | null | null | -1 | 2026-07-01T11:29:45.298029+00:00 |
scses-tissue-survivorship-canary-lr-ref-se-guided-v2 | pipeline/molecule_counter.py + stage_a_count.py (guided SiCeLoRe isobam) | N/A (bioinformatics pipeline: STARsolo + SiCeLoRe-2.1 + minimap2-2.17) | {"delta": 5, "types": "SE", "sicelore_mode": "guided --cellRangerBCs", "cell_whitelist": "STARsolo filtered 1122"} | [] | CORRECTED canary long-read SE PSI reference. Supersedes v1: v1's SiCeLoRe ran WITHOUT --cellRangerBCs so ONT barcodes were matched to the full 6.79M 10x v3 whitelist and mis-assigned to Levenshtein-1 neighbours -> LR cells did NOT correspond to SR cells (2/1122 overlap). This v2 runs SiCeLoRe guided by the STARsolo SR ... | ["scses-tissue-survivorship", "canary", "long-read-reference", "guided-barcode-fix", "SE"] | {"experiment_name": "scses-tissue-survivorship", "job_id": "puhti:35338705(sicelore-guided)+35339089(count)", "cluster": "puhti", "artifact_status": "partial", "canary": true} | 2026-07-01T12:05:41.105839+00:00 | null | null | null | null | null | null | -1 | 2026-07-01T12:05:41.105839+00:00 |
jinyang-junctioncounts-psi-s1-3v3-dpsi-v1 | 02_quantify_psi.sbatch + 03_dexseq_stats.sbatch + DEXSeq_comparison.R | junctionCounts (Wallace et al. 2024) + DEXSeq negative-binomial GLM (no ML model) | {"min_jc": 15, "min_psi": 0.1, "ri_span": 0.03, "sig_dpsi": 0.1, "sig_qval": 0.05, "single_end": true, "stranded": false} | [] | junctionCounts + DEXSeq differential splicing for S1 3v3 (HFD1-3 vs ND1-3) mouse Smart-seq2 pseudo-bulk BAMs. 33989 events annotated -> 14389 through DEXSeq -> 10336 tested -> 20 significant (|dPSI|>=0.1, q<=0.05). CLASP2: only MF.0003946 testable (HFD=ND PSI=1, dPSI=0, q=1); both SE cassette exons below min_jc=15 and ... | ["jinyang-junctioncounts-psi", "splicing", "psi", "dexseq", "junctioncounts", "s1-3v3", "hfd-vs-nd", "mouse"] | {"tool": "junctionCounts (Wallace et al., NAR Genom Bioinform 2024) + DEXSeq", "reference": "gencode.vM20.basic.annotation.gtf (GRCm38/mm10)", "experiment_name": "jinyang-junctioncounts-psi", "job_id": "turso:75068024", "cluster": "turso", "artifact_status": "final", "canary": false, "samples": "HFD1,HFD2,HFD3 vs ND1,N... | 2026-07-03T12:25:33.326956+00:00 | null | null | null | null | null | null | -1 | 2026-07-03T12:25:33.326956+00:00 |
scses-tissue-survivorship-lr-ref-se-cancer-full-v1 | pipeline/stage_a_count.py | N/A (long-read gold-standard reference) | {} | [] | Cancer LR ref on SCSES SE events. 296753 pairs. 3750 cells. n_LR strata: [0,1)=90539 [1,3)=174552 [3,5)=15571 [5,10)=9155 [10,20)=3782 [20,inf)=3154. Survivorship-critical [3,10)=24726. | ["scses-tissue-survivorship", "lr-reference", "SE", "cancer-panel"] | {"experiment_name": "scses-tissue-survivorship", "cluster": "puhti", "artifact_status": "final", "canary": false} | 2026-07-03T20:01:06.501293+00:00 | null | null | null | null | null | null | -1 | 2026-07-03T20:01:06.501293+00:00 |
scses-tissue-survivorship-delta-mse-se-cancer-v1 | pipeline/delta_mse_matcher.py | SCSES imputed vs raw PSI (10x SR, SE, hg38) | {} | [] | HEADLINE: SCSES imputed WORSE than raw PSI across ALL n_LR strata (ΔMSE>0). 20972 pairs. Overall ΔMSE=0.25705. {'[1,3)': {'n': 18015, 'mean_delta_mse': 0.25338}, '[10,20)': {'n': 423, 'mean_delta_mse': 0.32134}, '[20,inf)': {'n': 262, 'mean_delta_mse': 0.23517}, '[3,5)': {'n': 1407, 'mean_delta_mse': 0.26119}, '[5,10)'... | ["scses-tissue-survivorship", "delta-mse", "headline", "SE"] | {"experiment_name": "scses-tissue-survivorship", "cluster": "puhti", "artifact_status": "final", "canary": false, "overall_mean_delta_mse": 0.25705, "strata_summary": {"[1,3)": {"n": 18015, "mean_delta_mse": 0.25338}, "[10,20)": {"n": 423, "mean_delta_mse": 0.32134}, "[20,inf)": {"n": 262, "mean_delta_mse": 0.23517}, "... | 2026-07-03T21:40:02.360880+00:00 | null | null | null | null | null | null | -1 | 2026-07-03T21:40:02.360880+00:00 |
jasec-python-vs-julia-concordance-v1 | run_python_liver.sbatch + compare_jasec_outputs.py | JAseC (software, not an ML model) | {"python_port_sha": "b4766e6-clean_side_softwarn_patch", "julia_ref": "patched Julia (PATCH B1), jasec_full/output", "samples": 17, "shared_assembled_gtf": "reused from Julia run"} | [] | Software-equivalence concordance: the JAseC Python port (HEAD b4766e6 + clean_side soft-warn patch) vs the original Julia JAseC, run end-to-end on the real 17-sample liver 10x 5'-scRNA-seq dataset (same BAMs, same reference GTF, same StringTie assembled annotation reused from the Julia run for a fair core-pipeline diff... | ["jasec", "python-vs-julia", "concordance", "software-equivalence", "liver-10x"] | {"experiment_name": "jasec-python-vs-julia", "job_id": "turso:75092523", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-07-12T20:57:55.990007+00:00 | null | null | null | null | null | null | -1 | 2026-07-12T20:57:55.990007+00:00 |
within-site-subtypes-results-v1 | 05_existence_gate.py + 06_cluster_stability.py | N/A — unsupervised clustering (SigClust + gap + PAM on sqrt-JSD) | {"sigclust_sims": 1000, "gap_B": 100, "bootstrap": 1000, "pred_strength_splits": 50, "seed": 20260709} | [] | Within-site (Ome/Asc/Per, PDS, n=30/site) subtype existence-gate + stability. PRIMARY RESULT: 0/6 primary cells pass -> no stable within-site subtypes in TPM or PSI. | ["within-site-subtypes", "clustering", "negative-result", "hgsoc", "splicing"] | {"experiment_name": "within-site-subtypes", "cluster": "local (ePouta subset + local clustering)", "artifact_status": "final", "canary": false} | 2026-07-13T10:41:37.170312+00:00 | within-site-subtypes | null | analysis_result | table | null | null | -1 | 2026-07-13T10:36:03.675050+00:00 |
within-site-subtypes-composition-v1 | 23_composition_association.py (+ 20-22,24,25) | N/A — ESTIMATE (ssGSEA) + PCoA + partial Spearman + vegan::adonis2 | {"estimate_platform": "illumina (relative ESTIMATEScore, no absolute purity)", "ensg_to_symbol": "org.Hs.eg.db", "pcoa": "classical MDS top-3 (sum|lambda| denom)", "association": "Spearman + partial (| coverage,star_uniq,chem2v4)", "adonis": "vegan::adonis2 by=margin 9999 perm + betadisper", "seed": 20260713, "bonferro... | [] | Within-site (Ome/Asc/Per, PDS, n=30/site) continuous-axis-vs-composition test. RESULT (confirmatory, prereg ec64515 + Amendment 1 72da6ff): all 3 PRIMARY PSI cells + all 3 TPM cells = composition_axis. The dominant continuous axis of within-site splicing (PSI) and expression (TPM) variation is a tumor-composition (ESTI... | ["within-site-subtypes", "composition", "estimate", "splicing", "hgsoc", "confirmatory", "positive-result"] | {"experiment_name": "within-site-subtypes", "cluster": "local", "artifact_status": "final", "canary": false} | 2026-07-14T13:49:46.442005+00:00 | within-site-subtypes | null | analysis_result | table | null | null | -1 | 2026-07-14T13:49:46.442005+00:00 |
jinyang-gse319320-splicekit-psi-canary-v1 | run_splicekit.sh (setup annotation features introns events edgeR) | n/a (splicing quantification tool) | {"library_strand": "SECOND_READ_TRANSCRIPTION_STRAND (featureCounts -s 2, reverse/fr-firststrand)", "psi_minimum_reads": 10, "genome": "GRCh38 Ensembl-113 (pybio; same annotation as STAR alignment)", "platform": "desktop", "samples": "ctrl GSM9515537,GSM9515539 | KO GSM9515538,GSM9515540"} | [] | CANARY (2 control + 2 ADAR1-KO) per-sample PSI matrix from splicekit's native pipeline on GSE319320 STAR BAMs (GRCh38 Ensembl-113). Validates the pipeline E2E before the full 12-sample run. RI blind-spot fix engaged: 310,901 annotated-but-never-spliced introns added to the 260,850 observed. PSI = mean(inclusion)/(mean(... | ["splicekit", "psi-matrix", "gse319320", "human", "adar1", "canary", "retained-intron", "concordance"] | {"tool": "splicekit (fork wangdepin/splicekit-shiba @ fix-ri-blind-spot, commit 1e27899; patched: _normalize_chr no-op for Ensembl contigs, fireducks->pandas)", "experiment_name": "jinyang-gse319320-splicekit-psi", "job_id": "turso:75136095", "cluster": "turso", "artifact_status": "partial", "canary": true} | 2026-07-16T10:26:05.213308+00:00 | null | null | null | null | null | null | -1 | 2026-07-16T10:26:05.213308+00:00 |
jinyang-gse319320-splicekit-psi-full-v1 | run_splicekit.sh (setup annotation features introns events edgeR) | n/a (splicing quantification tool) | {"library_strand": "SECOND_READ_TRANSCRIPTION_STRAND (featureCounts -s 2, reverse/fr-firststrand)", "psi_minimum_reads": 10, "min_intron_len": 70, "genome": "GRCh38 Ensembl-113 (pybio; same GTF as the STAR alignment and as the Shiba run)", "platform": "desktop", "control": "GSM9515537,GSM9515539,GSM9515541,GSM9515543,G... | [] | TWO CONFIGS: `default` = all 530,503 events, as splicekit wrote them. `filtered` = 182,761 events (34.45%), keeping only rows with at least one PSI > 0 — i.e. dropping 332,760 all-NA rows (62.73%, never cleared the 10-read gate), 5,788 all-zero rows (1.09%) and 9,194 mixed NA/0 rows (1.73%). Reproduce with scripts/filt... | ["splicekit", "psi-matrix", "gse319320", "human", "adar1", "retained-intron", "concordance"] | {"tool": "splicekit (fork wangdepin/splicekit-shiba @ fix-ri-blind-spot, commit 1e27899; patched: _normalize_chr no-op for Ensembl contigs, fireducks->pandas)", "experiment_name": "jinyang-gse319320-splicekit-psi", "job_id": "turso:75136243", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-07-16T12:31:28.310754+00:00 | null | null | null | null | null | null | -1 | 2026-07-16T11:41:24.444975+00:00 |
jinyang-gse319320-splicekit-psi-vs-shiba-concordance-v1 | compare_splicekit_shiba.py | n/a (splicing quantification concordance) | {"match_key": "pos_id with 'chr' prefix stripped (implicitly (event_type, coords))", "min_reps_for_dpsi": 3, "psi_gate": "both tools: score if a side averages >= 10 reads, else NA/blank -> NaN", "control": "GSM9515537,539,541,543,545,547", "ADAR1_KO": "GSM9515538,540,542,544,546,548"} | ["depinwang/jinyang-gse319320-splicekit-psi-full-v1", "depinwang/jinyang-gse319320-shiba-psi-full-v1"] | Event-level concordance between splicekit's native PSI pipeline and Shiba v0.8.2, run on the IDENTICAL 12 GSE319320 STAR BAMs (6 control / 6 ADAR1-KO), same GTF (GRCh38 Ensembl-113), same coverage gate (10 reads) and intron floor (70nt) — so differences are method-level, not threshold artifacts. Union of both tools' ev... | ["splicekit", "shiba", "concordance", "psi-matrix", "gse319320", "human", "adar1", "retained-intron"] | {"tool": "splicekit (fork wangdepin/splicekit-shiba @ fix-ri-blind-spot, 1e27899) vs Shiba v0.8.2", "experiment_name": "jinyang-gse319320-splicekit-psi", "job_id": "turso:75136243", "cluster": "turso", "artifact_status": "final", "canary": false} | 2026-07-16T12:03:26.647636+00:00 | null | null | null | null | null | null | -1 | 2026-07-16T12:02:45.158507+00:00 |
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RACA-PROJECT-MANIFEST
Central registry of all datasets in the depinwang organization.
- Total Datasets Tracked: 102
- Last Updated: 2026-07-19T09:59:49.897506+00:00
Usage
from datasets import load_dataset
manifest = load_dataset("depinwang/RACA-PROJECT-MANIFEST", split="train")
print(f"Tracking {len(manifest)} datasets")
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