Datasets:

tahoebio
/

replogle-nadig-de-rhaister

target large_string	feature large_string	target_mean float32	ref_mean float32	target_membership int32	ref_membership int32	fold_change float64	percent_change float64	p_value float64	statistic float64	fdr float64	cell_line large_string	gem_group int32	n_cells_stratum int32	n_reference_cells int32
AAR2	0	1.281022	0.763952	2	105	0.745742	0.676836	0.478543	136	0.861202	hepg2	1	1,798	105
AAR2	1	1.733201	0.92826	2	105	0.900838	0.867151	0.334932	147	0.861202	hepg2	1	1,798	105
AAR2	2	0.282671	0.481556	2	105	-0.768581	-0.413006	0.644657	85.5	0.864228	hepg2	1	1,798	105
AAR2	3	2.279362	1.608276	2	105	0.503115	0.41727	0.427307	140	0.861202	hepg2	1	1,798	105
AAR2	4	0.707601	0.150577	2	105	2.232431	3.699252	0.02884	177	0.861202	hepg2	1	1,798	105
AAR2	5	0.513436	0.47612	2	105	0.108861	0.078377	0.792	116.5	0.920859	hepg2	1	1,798	105
AAR2	6	0.282671	0.145424	2	105	0.958863	0.943777	0.530882	126	0.861202	hepg2	1	1,798	105
AAR2	7	1.014815	0.271933	2	105	1.899895	2.731861	0.053253	180	0.861202	hepg2	1	1,798	105
AAR2	8	0	0.448571	2	105	null	-1	0.164199	47	0.861202	hepg2	1	1,798	105
AAR2	9	0	0.273588	2	105	null	-1	0.286938	64	0.861202	hepg2	1	1,798	105
AAR2	10	5.937101	4.136332	2	105	0.521407	0.435354	0.339785	147	0.861202	hepg2	1	1,798	105
AAR2	11	0	0.368794	2	105	null	-1	0.216525	55	0.861202	hepg2	1	1,798	105
AAR2	12	0	0.145425	2	105	null	-1	0.471312	82	0.861202	hepg2	1	1,798	105
AAR2	13	2.777878	1.988788	2	105	0.482094	0.396769	0.542036	132	0.861202	hepg2	1	1,798	105
AAR2	14	1.014815	0.390626	2	105	1.377359	1.597923	0.125072	168	0.861202	hepg2	1	1,798	105
AAR2	15	0.513436	0.643798	2	105	-0.326423	-0.202489	0.887267	98.5	0.959373	hepg2	1	1,798	105
AAR2	16	1.519254	1.714006	2	105	-0.174009	-0.113624	0.670276	86	0.869397	hepg2	1	1,798	105
AAR2	17	0	0.135351	2	105	null	-1	0.447295	80	0.861202	hepg2	1	1,798	105
AAR2	18	1.414223	0.198527	2	105	2.832599	6.123565	0.006003	206	0.861202	hepg2	1	1,798	105
AAR2	19	0	0.183666	2	105	null	-1	0.391608	75	0.861202	hepg2	1	1,798	105
AAR2	20	0	0.354593	2	105	null	-1	0.231084	57	0.861202	hepg2	1	1,798	105
AAR2	21	1.519254	1.575055	2	105	-0.052039	-0.035428	0.791193	93	0.920469	hepg2	1	1,798	105
AAR2	22	1.519254	1.336401	2	105	0.18501	0.136825	0.917445	110	0.972056	hepg2	1	1,798	105
AAR2	23	0.331285	0.18463	2	105	0.843435	0.794317	0.536191	127.5	0.861202	hepg2	1	1,798	105
AAR2	24	0.707601	1.573878	2	105	-1.153317	-0.55041	0.095285	32	0.861202	hepg2	1	1,798	105
AAR2	25	0	0.183537	2	105	null	-1	0.413189	77	0.861202	hepg2	1	1,798	105
AAR2	26	0	0.449833	2	105	null	-1	0.170233	48	0.861202	hepg2	1	1,798	105
AAR2	27	0.282671	0.356588	2	105	-0.335136	-0.207291	0.819569	95.5	0.933351	hepg2	1	1,798	105
AAR2	28	1.046107	0.244501	2	105	2.09712	3.278546	0.03718	183	0.861202	hepg2	1	1,798	105
AAR2	29	15.71878	19.774475	2	105	-0.33115	-0.205098	0.274568	57	0.861202	hepg2	1	1,798	105
AAR2	30	1.593813	0.518774	2	105	1.619305	2.07227	0.176754	162	0.861202	hepg2	1	1,798	105
AAR2	31	0.713398	0.560013	2	105	0.349246	0.273895	0.755297	118.5	0.90264	hepg2	1	1,798	105
AAR2	32	0.282671	0.501794	2	105	-0.827971	-0.436679	0.490512	76	0.861202	hepg2	1	1,798	105
AAR2	33	0	0.22591	2	105	null	-1	0.322455	68	0.861202	hepg2	1	1,798	105
AAR2	34	0.331285	0.19592	2	105	0.757809	0.690921	0.59921	124	0.861662	hepg2	1	1,798	105
AAR2	35	0	0.162398	2	105	null	-1	0.435682	79	0.861202	hepg2	1	1,798	105
AAR2	36	0.282671	0.418313	2	105	-0.565461	-0.324261	0.750623	91.5	0.90264	hepg2	1	1,798	105
AAR2	37	1.281022	1.071705	2	105	0.257386	0.195311	0.880478	112	0.954678	hepg2	1	1,798	105
AAR2	38	0.331285	0.88519	2	105	-1.417913	-0.625747	0.257498	56	0.861202	hepg2	1	1,798	105
AAR2	39	5.518802	6.950697	2	105	-0.332803	-0.206007	0.427443	70	0.861202	hepg2	1	1,798	105
AAR2	40	1.336067	0.93375	2	105	0.516884	0.430861	0.702003	122	0.877784	hepg2	1	1,798	105
AAR2	41	28.350132	21.149487	2	105	0.422733	0.340464	0.201736	161	0.861202	hepg2	1	1,798	105
AAR2	42	2.464828	1.528596	2	105	0.68928	0.612479	0.387039	143	0.861202	hepg2	1	1,798	105
AAR2	43	0.707601	0.536281	2	105	0.399948	0.31946	0.857306	113	0.948701	hepg2	1	1,798	105
AAR2	44	1.281022	1.427136	2	105	-0.155828	-0.102383	0.587191	81	0.861662	hepg2	1	1,798	105
AAR2	45	1.414223	1.37789	2	105	0.037548	0.026368	0.86288	97	0.948701	hepg2	1	1,798	105
AAR2	46	0.331285	0.487314	2	105	-0.556777	-0.320181	0.616539	83.5	0.864228	hepg2	1	1,798	105
AAR2	47	0.707601	0.909412	2	105	-0.361998	-0.221914	0.348071	64	0.861202	hepg2	1	1,798	105
AAR2	48	2.12688	1.861879	2	105	0.191979	0.14233	0.844966	114	0.941175	hepg2	1	1,798	105
AAR2	49	0.282671	0.33259	2	105	-0.234623	-0.150093	0.907634	100	0.969861	hepg2	1	1,798	105
AAR2	50	0.821252	0.951777	2	105	-0.212798	-0.137138	0.95377	108	0.98795	hepg2	1	1,798	105
AAR2	51	0	0.180954	2	105	null	-1	0.391608	75	0.861202	hepg2	1	1,798	105
AAR2	52	1.014815	0.784886	2	105	0.370662	0.292946	0.806346	116	0.927455	hepg2	1	1,798	105
AAR2	53	5.754386	3.48705	2	105	0.722655	0.650216	0.193707	162	0.861202	hepg2	1	1,798	105
AAR2	54	1.046107	0.540505	2	105	0.952652	0.935427	0.337589	146	0.861202	hepg2	1	1,798	105
AAR2	55	0	0.301479	2	105	null	-1	0.270183	62	0.861202	hepg2	1	1,798	105
AAR2	56	0.892347	0.294915	2	105	1.597305	2.025775	0.441962	135.5	0.861202	hepg2	1	1,798	105
AAR2	57	0.282671	0.850135	2	105	-1.588569	-0.667499	0.185828	47.5	0.861202	hepg2	1	1,798	105
AAR2	58	2.120531	0.668992	2	105	1.664364	2.169739	0.057673	186	0.861202	hepg2	1	1,798	105
AAR2	59	0.821252	1.295999	2	105	-0.658168	-0.366317	0.7035	88	0.877784	hepg2	1	1,798	105
AAR2	60	1.014815	0.288242	2	105	1.815863	2.520701	0.065613	176	0.861202	hepg2	1	1,798	105
AAR2	61	0.707601	0.239753	2	105	1.561389	1.951379	0.094998	169	0.861202	hepg2	1	1,798	105
AAR2	62	0	0.151564	2	105	null	-1	0.424317	78	0.861202	hepg2	1	1,798	105
AAR2	63	0	0.219985	2	105	null	-1	0.322455	68	0.861202	hepg2	1	1,798	105
AAR2	64	0.282671	0.66137	2	105	-1.226334	-0.572598	0.322923	62.5	0.861202	hepg2	1	1,798	105
AAR2	65	0	0.231302	2	105	null	-1	0.341264	70	0.861202	hepg2	1	1,798	105
AAR2	66	0	0.623162	2	105	null	-1	0.12093	39	0.861202	hepg2	1	1,798	105
AAR2	67	0	0.339974	2	105	null	-1	0.262049	61	0.861202	hepg2	1	1,798	105
AAR2	68	1.022197	1.119366	2	105	-0.131008	-0.086807	1	105.5	1	hepg2	1	1,798	105
AAR2	69	0	0.085848	2	105	null	-1	0.565498	89	0.861202	hepg2	1	1,798	105
AAR2	70	0	0.141261	2	105	null	-1	0.447295	80	0.861202	hepg2	1	1,798	105
AAR2	71	0.707601	0.728774	2	105	-0.042536	-0.029053	0.879539	98	0.954678	hepg2	1	1,798	105
AAR2	72	0.513436	0.419506	2	105	0.291492	0.223906	0.730127	119.5	0.890021	hepg2	1	1,798	105
AAR2	73	0	0.191022	2	105	null	-1	0.402288	76	0.861202	hepg2	1	1,798	105
AAR2	74	0.707601	0.256105	2	105	1.466201	1.762933	0.122096	163	0.861202	hepg2	1	1,798	105
AAR2	75	0.513436	0.957323	2	105	-0.898821	-0.463675	0.539561	78	0.861202	hepg2	1	1,798	105
AAR2	76	0.282671	0.544387	2	105	-0.94551	-0.480754	0.453688	73	0.861202	hepg2	1	1,798	105
AAR2	77	0.707601	0.433856	2	105	0.705718	0.630956	0.505857	133	0.861202	hepg2	1	1,798	105
AAR2	78	0.513436	0.511307	2	105	0.005994	0.004163	0.866727	112.5	0.951503	hepg2	1	1,798	105
AAR2	79	2.446442	1.639214	2	105	0.577681	0.492449	0.316591	149	0.861202	hepg2	1	1,798	105
AAR2	80	0.331285	1.825549	2	105	-2.462185	-0.818529	0.05317	20.5	0.861202	hepg2	1	1,798	105
AAR2	81	3.157187	3.565835	2	105	-0.1756	-0.114601	0.482949	74	0.861202	hepg2	1	1,798	105
AAR2	82	3.789635	4.059423	2	105	-0.099216	-0.06646	0.67044	86	0.869397	hepg2	1	1,798	105
AAR2	83	0	0.122842	2	105	null	-1	0.471312	82	0.861202	hepg2	1	1,798	105
AAR2	84	5.519558	6.452206	2	105	-0.22524	-0.144547	0.588817	81	0.861662	hepg2	1	1,798	105
AAR2	85	2.060466	2.913649	2	105	-0.499856	-0.292823	0.339785	63	0.861202	hepg2	1	1,798	105
AAR2	86	2.120531	2.115127	2	105	0.003681	0.002555	0.972476	103	0.995282	hepg2	1	1,798	105
AAR2	87	1.281022	0.527393	2	105	1.280344	1.428969	0.185867	160	0.861202	hepg2	1	1,798	105
AAR2	88	0.331285	0.694445	2	105	-1.067787	-0.52295	0.385529	67.5	0.861202	hepg2	1	1,798	105
AAR2	89	2.744091	4.269002	2	105	-0.637571	-0.357206	0.126104	38	0.861202	hepg2	1	1,798	105
AAR2	90	0.513436	0.235588	2	105	1.123918	1.179381	0.412176	136	0.861202	hepg2	1	1,798	105
AAR2	91	1.519254	2.263101	2	105	-0.574938	-0.328685	0.363527	65	0.861202	hepg2	1	1,798	105
AAR2	92	0.282671	0.612997	2	105	-1.116756	-0.538871	0.421785	70.5	0.861202	hepg2	1	1,798	105
AAR2	93	5.999498	5.235445	2	105	0.19653	0.145938	0.844985	114	0.941175	hepg2	1	1,798	105
AAR2	94	48.686897	54.8778	2	105	-0.172689	-0.112813	0.284799	58	0.861202	hepg2	1	1,798	105
AAR2	95	1.736826	0.507576	2	105	1.774757	2.421804	0.136128	168	0.861202	hepg2	1	1,798	105
AAR2	96	1.733201	0.655141	2	105	1.403561	1.645538	0.081541	180	0.861202	hepg2	1	1,798	105
AAR2	97	0.282671	0.836744	2	105	-1.565663	-0.662178	0.205415	50	0.861202	hepg2	1	1,798	105
AAR2	98	0.821252	0.957336	2	105	-0.221199	-0.142148	1	105.5	1	hepg2	1	1,798	105
AAR2	99	0.331285	0.278864	2	105	0.248512	0.187981	0.840185	113	0.941175	hepg2	1	1,798	105

End of preview. Expand in Data Studio

Replogle-Nadig CRISPR Screen Differential Expression Summary Statistics

Differential-expression summary statistics for the Replogle-Nadig genome-scale CRISPR screen, which includes 4 cell lines and ~2,000 gene knockdowns. Used to train Rhaister, the data are per-gene fold changes, significance, and pseudobulk deltas summarized from raw single cells. The four cell lines are hepg2, jurkat, k562, and rpe1 and the perturbation is a CRISPR knockdown of a target gene.

The repository contains two tables: pdex and cell_eval.

`pdex` per-gene differential expression (long format)

from datasets import load_dataset
pdex = load_dataset("tahoebio/replogle-nadig-de-rhaister", "pdex", streaming=True, split="train")

One row per (cell line, gem_group, target KD, gene). ~1.5 B rows total.

Column	Description
`cell_line`	Cell line (`hepg2`, `jurkat`, `k562`, `rpe1`).
`gem_group`	Sequencing batch (1–56).
`target`	CRISPR knockdown target gene.
`feature`	Measured gene symbol.
`fold_change`	log2 fold change, `log2(target_mean / ref_mean)`. `-inf` where `target_mean = 0`.
`percent_change`	`(target_mean − ref_mean) / ref_mean`.
`p_value`	Mann–Whitney U p-value, perturbed vs. non-targeting control.
`statistic`	Mann–Whitney U statistic.
`fdr`	Benjamini–Hochberg adjusted p-value.
`target_mean` / `ref_mean`	Mean expression in the perturbed / control group.
`target_membership` / `ref_membership`	Cell counts in the perturbed / control group.
`n_cells_stratum` / `n_reference_cells`	Stratum and reference cell counts.

`cell_eval` pseudobulk expression deltas (wide format)

cell_eval = load_dataset("tahoebio/replogle-nadig-de-rhaister", "cell_eval", streaming=True, split="train")

One row per (cell line, gem_group, target gene). Columns cell_line, gem_group, gene, then one column per measured gene (~6,546) holding the pseudobulk delta mean(perturbed) − mean(control) on the linear (normalized) scale.

Definition & filtering criteria

definition/ holds the dataset definition (dataset.toml) and the holdout split TOMLs (split_0–split_3). It records the cell/treatment columns (cell_line, and gene as the treatment), the 2,000 highly-variable genes used for analysis (hvg_2k_genes.json), and the feature_names.json map from pdex's integer feature indices to gene symbols. The compositional split holds out a (cell line, gene) pair only when its cell line is in the holdout set and its target is in that cell line's held-out list, so each test cell line and target is still seen individually in training.

Source

Downloads last month: 127

Datasets:

tahoebio
/

replogle-nadig-de-rhaister

Replogle-Nadig CRISPR Screen Differential Expression Summary Statistics

`pdex` per-gene differential expression (long format)

`cell_eval` pseudobulk expression deltas (wide format)

Definition & filtering criteria

Source

Models trained or fine-tuned on tahoebio/replogle-nadig-de-rhaister

tahoebio/Rhaister

Collection including tahoebio/replogle-nadig-de-rhaister

Rhaister

Replogle-Nadig CRISPR Screen Differential Expression Summary Statistics

pdex per-gene differential expression (long format)

cell_eval pseudobulk expression deltas (wide format)

Definition & filtering criteria

Source

Models trained or fine-tuned on tahoebio/replogle-nadig-de-rhaister

Collection including tahoebio/replogle-nadig-de-rhaister

`pdex` per-gene differential expression (long format)

`cell_eval` pseudobulk expression deltas (wide format)