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_type large_string	donor large_string
4-1BBL	TSPAN6	0	0.000862	300	1,608	null	-1	0.541869	240,900	1	B_Intermediate_Memory	Donor1
4-1BBL	TNMD	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	DPM1	0.133132	0.170568	300	1,608	-0.357487	-0.219477	0.19858	233,553.5	0.891434	B_Intermediate_Memory	Donor1
4-1BBL	SCYL3	0.111943	0.207888	300	1,608	-0.893046	-0.461524	0.000376	218,928.5	0.022998	B_Intermediate_Memory	Donor1
4-1BBL	C1orf112	0.085505	0.10863	300	1,608	-0.345348	-0.212882	0.362136	236,724.5	1	B_Intermediate_Memory	Donor1
4-1BBL	FGR	0.018656	0.031667	300	1,608	-0.763353	-0.410874	0.102649	236,575.5	0.670242	B_Intermediate_Memory	Donor1
4-1BBL	CFH	0.002313	0.00259	300	1,608	-0.162929	-0.10679	0.917087	241,104	1	B_Intermediate_Memory	Donor1
4-1BBL	FUCA2	0.041467	0.036173	300	1,608	0.197025	0.146332	0.621347	242,798	1	B_Intermediate_Memory	Donor1
4-1BBL	GCLC	0.111704	0.130757	300	1,608	-0.227207	-0.145713	0.523414	237,827	1	B_Intermediate_Memory	Donor1
4-1BBL	NFYA	0.116022	0.150163	300	1,608	-0.372122	-0.227355	0.161957	233,286	0.859678	B_Intermediate_Memory	Donor1
4-1BBL	STPG1	0.037072	0.043387	300	1,608	-0.226928	-0.145547	0.577383	239,360	1	B_Intermediate_Memory	Donor1
4-1BBL	NIPAL3	0.200711	0.241462	300	1,608	-0.266675	-0.168767	0.307522	234,594.5	1	B_Intermediate_Memory	Donor1
4-1BBL	LAS1L	0.096634	0.166938	300	1,608	-0.788698	-0.421134	0.005185	225,044	0.124346	B_Intermediate_Memory	Donor1
4-1BBL	ENPP4	0.038067	0.053397	300	1,608	-0.488217	-0.287094	0.200342	236,337.5	0.895856	B_Intermediate_Memory	Donor1
4-1BBL	SEMA3F	0	0.000431	300	1,608	null	-1	0.666836	241,050	1	B_Intermediate_Memory	Donor1
4-1BBL	CFTR	0	0.003454	300	1,608	null	-1	0.221166	240,000	0.939418	B_Intermediate_Memory	Donor1
4-1BBL	ANKIB1	0.885528	1.130765	300	1,608	-0.352689	-0.216877	0.00434	217,166	0.111264	B_Intermediate_Memory	Donor1
4-1BBL	CYP51A1	0.249981	0.302673	300	1,608	-0.275942	-0.174089	0.152396	231,396	0.824767	B_Intermediate_Memory	Donor1
4-1BBL	KRIT1	0.32967	0.403408	300	1,608	-0.291218	-0.182788	0.101524	229,011.5	0.665526	B_Intermediate_Memory	Donor1
4-1BBL	RAD52	0.061685	0.120048	300	1,608	-0.960616	-0.486162	0.001613	224,919.5	0.056536	B_Intermediate_Memory	Donor1
4-1BBL	MYH16	0	0.002158	300	1,608	null	-1	0.333942	240,450	1	B_Intermediate_Memory	Donor1
4-1BBL	BAD	0.011619	0.015714	300	1,608	-0.435478	-0.260551	0.570105	239,965	1	B_Intermediate_Memory	Donor1
4-1BBL	LAP3	0.952886	1.20729	300	1,608	-0.341397	-0.210724	0.00905	219,028	0.175787	B_Intermediate_Memory	Donor1
4-1BBL	CD99	0.126142	0.144337	300	1,608	-0.194394	-0.12606	0.418982	236,704	1	B_Intermediate_Memory	Donor1
4-1BBL	HS3ST1	0.01065	0.022153	300	1,608	-1.056699	-0.519269	0.141605	237,671.5	0.797939	B_Intermediate_Memory	Donor1
4-1BBL	AOC1	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	WNT16	0.028114	0.029563	300	1,608	-0.072489	-0.049004	0.840622	241,782	1	B_Intermediate_Memory	Donor1
4-1BBL	HECW1	0.018656	0.016226	300	1,608	0.201316	0.149747	0.60479	242,366	1	B_Intermediate_Memory	Donor1
4-1BBL	MAD1L1	0.296022	0.467998	300	1,608	-0.660796	-0.367471	0.00007	211,193	0.007116	B_Intermediate_Memory	Donor1
4-1BBL	LASP1	0.220781	0.322862	300	1,608	-0.548301	-0.316175	0.005176	221,513	0.124335	B_Intermediate_Memory	Donor1
4-1BBL	SNX11	0.039836	0.064551	300	1,608	-0.69636	-0.382873	0.059176	233,585.5	0.478846	B_Intermediate_Memory	Donor1
4-1BBL	TMEM176A	0	0.000862	300	1,608	null	-1	0.541869	240,900	1	B_Intermediate_Memory	Donor1
4-1BBL	M6PR	0.095583	0.202181	300	1,608	-1.080814	-0.527238	0.000028	215,247	0.00383	B_Intermediate_Memory	Donor1
4-1BBL	KLHL13	0.002313	0.003161	300	1,608	-0.450601	-0.268262	0.950723	241,253	1	B_Intermediate_Memory	Donor1
4-1BBL	CYP26B1	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	ICA1	0	0.003847	300	1,608	null	-1	0.252605	240,150	0.997564	B_Intermediate_Memory	Donor1
4-1BBL	DBNDD1	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	ALS2	0.07033	0.090607	300	1,608	-0.365479	-0.223789	0.221932	235,643.5	0.94178	B_Intermediate_Memory	Donor1
4-1BBL	CASP10	0.300085	0.383207	300	1,608	-0.352754	-0.216912	0.128457	230,088	0.766841	B_Intermediate_Memory	Donor1
4-1BBL	CFLAR	2.020319	2.324475	300	1,608	-0.202322	-0.130849	0.056155	224,626	0.468699	B_Intermediate_Memory	Donor1
4-1BBL	TFPI	0.002313	0.002158	300	1,608	0.100417	0.072083	0.949786	241,254	1	B_Intermediate_Memory	Donor1
4-1BBL	NDUFAF7	0.075097	0.129947	300	1,608	-0.791103	-0.422098	0.005498	226,350	0.128904	B_Intermediate_Memory	Donor1
4-1BBL	RBM5	0.658754	0.776939	300	1,608	-0.238061	-0.152116	0.05458	225,325.5	0.460276	B_Intermediate_Memory	Donor1
4-1BBL	MTMR7	0.002313	0.000431	300	1,608	2.423589	4.365041	0.183196	241,854	0.86057	B_Intermediate_Memory	Donor1
4-1BBL	SLC7A2	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	ARF5	0.023374	0.03019	300	1,608	-0.369172	-0.225773	0.444861	238,890	1	B_Intermediate_Memory	Donor1
4-1BBL	SARM1	0.098118	0.101392	300	1,608	-0.047355	-0.032291	0.872088	240,387	1	B_Intermediate_Memory	Donor1
4-1BBL	POLDIP2	0.051549	0.061178	300	1,608	-0.247059	-0.157388	0.332429	237,350.5	1	B_Intermediate_Memory	Donor1
4-1BBL	PLXND1	0.002313	0.014401	300	1,608	-2.63823	-0.839375	0.05392	237,502	0.456805	B_Intermediate_Memory	Donor1
4-1BBL	AK2	0.198103	0.246397	300	1,608	-0.314732	-0.196	0.033867	227,128.5	0.335367	B_Intermediate_Memory	Donor1
4-1BBL	CD38	0.798814	1.083529	300	1,608	-0.439806	-0.262766	0.009733	220,575.5	0.183527	B_Intermediate_Memory	Donor1
4-1BBL	FKBP4	0.068045	0.115785	300	1,608	-0.766887	-0.412316	0.025433	230,266	0.276401	B_Intermediate_Memory	Donor1
4-1BBL	KDM1A	0.152217	0.186935	300	1,608	-0.296414	-0.185726	0.319301	235,226	1	B_Intermediate_Memory	Donor1
4-1BBL	RBM6	1.676295	2.295101	300	1,608	-0.453281	-0.26962	0.000006	201,988.5	0.001419	B_Intermediate_Memory	Donor1
4-1BBL	CAMKK1	0.018656	0.012398	300	1,608	0.589505	0.50473	0.243739	243,574	0.992167	B_Intermediate_Memory	Donor1
4-1BBL	RECQL	0.21563	0.32251	300	1,608	-0.580784	-0.3314	0.004034	220,816	0.106175	B_Intermediate_Memory	Donor1
4-1BBL	VPS50	0.348485	0.472827	300	1,608	-0.440214	-0.262975	0.01139	222,057.5	0.202755	B_Intermediate_Memory	Donor1
4-1BBL	HSPB6	0	0.000431	300	1,608	null	-1	0.666836	241,050	1	B_Intermediate_Memory	Donor1
4-1BBL	ARHGAP33	0	0.006307	300	1,608	null	-1	0.104954	239,100	0.676869	B_Intermediate_Memory	Donor1
4-1BBL	NDUFAB1	0.04006	0.063365	300	1,608	-0.661537	-0.367796	0.138149	235,198	0.784602	B_Intermediate_Memory	Donor1
4-1BBL	PDK4	0.002313	0	300	1,608	null	null	0.020683	242,004	0.240973	B_Intermediate_Memory	Donor1
4-1BBL	SLC22A16	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	ZMYND10	0.006956	0.000431	300	1,608	4.011888	15.132382	0.00112	243,462	0.044573	B_Intermediate_Memory	Donor1
4-1BBL	ABCB5	0.002313	0.001294	300	1,608	0.838005	0.787576	0.610498	241,554	1	B_Intermediate_Memory	Donor1
4-1BBL	ARX	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	SLC25A13	0.40425	0.522002	300	1,608	-0.368808	-0.225578	0.042713	225,647	0.393507	B_Intermediate_Memory	Donor1
4-1BBL	ST7	0.180266	0.229504	300	1,608	-0.348389	-0.214539	0.575011	237,937	1	B_Intermediate_Memory	Donor1
4-1BBL	CDC27	0.549266	0.629967	300	1,608	-0.197771	-0.128103	0.278498	232,468.5	1	B_Intermediate_Memory	Donor1
4-1BBL	SLC4A1	0	0.000431	300	1,608	null	-1	0.666836	241,050	1	B_Intermediate_Memory	Donor1
4-1BBL	CALCR	0	0.000862	300	1,608	null	-1	0.541869	240,900	1	B_Intermediate_Memory	Donor1
4-1BBL	HCCS	0.034273	0.038704	300	1,608	-0.175443	-0.114504	0.60909	239,520	1	B_Intermediate_Memory	Donor1
4-1BBL	DVL2	0.029504	0.036097	300	1,608	-0.290967	-0.182646	0.577291	239,425.5	1	B_Intermediate_Memory	Donor1
4-1BBL	PRSS22	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	UPF1	0.133975	0.170413	300	1,608	-0.347074	-0.213823	0.156143	232,756.5	0.837633	B_Intermediate_Memory	Donor1
4-1BBL	SKAP2	0.786127	1.231338	300	1,608	-0.647392	-0.361566	0.000003	201,597	0.000838	B_Intermediate_Memory	Donor1
4-1BBL	SLC25A5	0.220819	0.230408	300	1,608	-0.061325	-0.041617	0.742467	239,129	1	B_Intermediate_Memory	Donor1
4-1BBL	MCUB	0.537405	0.681704	300	1,608	-0.343136	-0.211674	0.0154	221,709.5	0.238183	B_Intermediate_Memory	Donor1
4-1BBL	POLR2J	0.031886	0.020981	300	1,608	0.603808	0.519723	0.197583	244,612.5	0.88891	B_Intermediate_Memory	Donor1
4-1BBL	DHX33	0.068695	0.086553	300	1,608	-0.333387	-0.206329	0.30683	236,552.5	1	B_Intermediate_Memory	Donor1
4-1BBL	MEOX1	0	0.001001	300	1,608	null	-1	0.666836	241,050	1	B_Intermediate_Memory	Donor1
4-1BBL	THSD7A	0	0.00259	300	1,608	null	-1	0.333942	240,450	1	B_Intermediate_Memory	Donor1
4-1BBL	LIG3	0.073644	0.074188	300	1,608	-0.010615	-0.00733	0.826405	242,166.5	1	B_Intermediate_Memory	Donor1
4-1BBL	RPAP3	0.203489	0.290242	300	1,608	-0.512309	-0.298901	0.007196	222,604	0.152563	B_Intermediate_Memory	Donor1
4-1BBL	ACSM3	0.239678	0.17308	300	1,608	0.469663	0.384786	0.235077	247,442.5	0.97315	B_Intermediate_Memory	Donor1
4-1BBL	REXO5	0.004632	0.00259	300	1,608	0.838739	0.788486	0.47053	241,908	1	B_Intermediate_Memory	Donor1
4-1BBL	CIAPIN1	0.047112	0.060084	300	1,608	-0.350881	-0.215895	0.240777	236,556.5	0.985366	B_Intermediate_Memory	Donor1
4-1BBL	SPPL2B	0.077583	0.105116	300	1,608	-0.438166	-0.261927	0.144042	233,853	0.807049	B_Intermediate_Memory	Donor1
4-1BBL	ATOSB	0.004632	0.00432	300	1,608	0.100529	0.072167	0.92859	241,308	1	B_Intermediate_Memory	Donor1
4-1BBL	COPZ2	0	0.002158	300	1,608	null	-1	0.333942	240,450	1	B_Intermediate_Memory	Donor1
4-1BBL	PRKAR2B	0.015331	0.010728	300	1,608	0.515051	0.429045	0.686845	241,923	1	B_Intermediate_Memory	Donor1
4-1BBL	MSL3	0.185536	0.203132	300	1,608	-0.130719	-0.086624	0.596809	237,796.5	1	B_Intermediate_Memory	Donor1
4-1BBL	CREBBP	1.023786	1.448755	300	1,608	-0.500899	-0.293334	0.000003	201,231.5	0.000905	B_Intermediate_Memory	Donor1
4-1BBL	TSPOAP1	0.035671	0.075228	300	1,608	-1.076507	-0.525824	0.008819	230,086	0.173	B_Intermediate_Memory	Donor1
4-1BBL	MPO	0	0	300	1,608	null	null	1	241,200	1	B_Intermediate_Memory	Donor1
4-1BBL	PON1	0	0.000431	300	1,608	null	-1	0.666836	241,050	1	B_Intermediate_Memory	Donor1
4-1BBL	GCFC2	0.130077	0.197181	300	1,608	-0.600152	-0.340316	0.03054	228,262	0.31246	B_Intermediate_Memory	Donor1
4-1BBL	WDR54	0.022393	0.007789	300	1,608	1.523484	1.874846	0.01122	245,745	0.201132	B_Intermediate_Memory	Donor1
4-1BBL	CROT	0.043876	0.060042	300	1,608	-0.452539	-0.269244	0.367963	237,671.5	1	B_Intermediate_Memory	Donor1
4-1BBL	ABCB4	0.124184	0.177662	300	1,608	-0.516657	-0.30101	0.038194	229,382.5	0.363638	B_Intermediate_Memory	Donor1
4-1BBL	KMT2E	1.557774	2.012954	300	1,608	-0.369828	-0.226125	0.000269	209,700.5	0.018462	B_Intermediate_Memory	Donor1

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Parse PBMC Cytokine Screen Differential Expression Summary Statistics

Differential-expression summary statistics for the Parse PBMC cytokine screen including 12 donors × 18 immune cell types × 90 cytokines. This data was used to train Rhaister. These are the statistics computed from the raw single cells of the Arc Institute ST-HVG-Parse dataset, including per-gene fold changes, significance, and pseudobulk deltas.

The cell context is a (donor, cell type) combination and the perturbation is a cytokine. The repo contains two tables (pdex and cell_eval) plus the dataset-definition files (filtering / split criteria) under definition/.

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

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

One row per (donor, cell type, cytokine, gene). ~774 M rows.

Column	Description
`donor`	Donor ID (e.g. `Donor1`).
`cell_type`	Immune cell type (e.g. `B_Intermediate_Memory`).
`target`	Cytokine treatment (e.g. `4-1BBL`).
`feature`	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, treated vs. control.
`statistic`	Mann–Whitney U statistic.
`fdr`	Benjamini–Hochberg adjusted p-value.
`target_mean` / `ref_mean`	Mean expression in the treated / control group.
`target_membership` / `ref_membership`	Cell counts in the treated / control group.

`cell_eval` pseudobulk expression deltas (wide format)

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

One row per (cell type, donor, cytokine). Columns cell_type, donor, cytokine, then one column per gene (~40,000) holding the pseudobulk delta mean(treated) − mean(control) on the linear (normalized) scale.

Definition & filtering criteria

definition/ contains the dataset definition (dataset.toml) and the holdout split TOMLs (split_0–split_4, plus donor splits). The composite cell context is built as {donor}__{cell_type}. The compositional split holds out a (cell context, cytokine) pair only when its context is in the holdout set and its cytokine is in that context's held-out list, so each test context and cytokine is still seen individually in training.

Source

Derived from the Arc Institute ST-HVG-Parse Parse PBMC cytokine dataset.

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Datasets:

tahoebio
/

parse-de-rhaister

Parse PBMC Cytokine 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/parse-de-rhaister

tahoebio/Rhaister

Collection including tahoebio/parse-de-rhaister

Rhaister

Parse PBMC Cytokine 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/parse-de-rhaister

Collection including tahoebio/parse-de-rhaister

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

`cell_eval` pseudobulk expression deltas (wide format)