arcinstitute/PIE_replogle_nadig_essential

PIE: Replogle-Nadig essential Perturb-seq

Differential-expression (DE) tables and the preprocessed dir for PIE, built from the CRISPRi essential-gene Perturb-seq screens in K562 and RPE1 (Replogle et al., 2022) and HepG2 and Jurkat (Nadig et al., 2025). This dataset is the test set of the PIE replogle_xdataset experiment and the train and test data of replogle_wdataset.

Datasets and knowledge sources: PIE collection

Contents

de/<cell_line>.parquet   per-cell-line DE, one row per (perturbation, gene)
preprocessed/            PIE preprocessed dir, with the context map contexts.yaml

Cell line	Cells	Perturbed genes	DE rows
K562	179,753	1,314	8,727,588
RPE1	167,372	1,453	9,650,826
HepG2	90,826	1,253	8,322,426
Jurkat	173,260	1,439	9,557,838

Controls are the non-targeting cells of each cell line.

de/

One parquet per cell line, from the pie process de stage (gpudge 0.7.0 on raw counts, grouped by target_gene against non-targeting, CP10k normalization, genes kept at ≥ 5 CPM).

Column	Description
target	perturbed gene
feature	measured gene
target_mean	mean expression in perturbed cells
ref_mean	mean expression in control cells
target_ncells	number of perturbed cells
ref_ncells	number of control cells
log2_fold_change	log2 fold change, perturbed vs. control
p_value	Mann-Whitney U test p-value
Ueffect	U-statistic effect size
p_adj	Benjamini-Hochberg adjusted p-value

preprocessed/

The PIE preprocessed dir (pie prep output, format version 1) that pie sources, pie train, pie eval and pie infer read: N = 5,459 rows, one per (cell line, perturbation) pair, over G = 6,642 genes and C = 4 cell lines.

File	Shape, dtype	Description
meta.json		gene axis, cell line and perturbation vocabularies, checksums, perturbation Ensembl ids
contexts.yaml		context -> Cellosaurus accession map; pie sources reads it for context_text
fold_changes.npy	(N, G) float32	linear fold change, 0 where untested
fdr.npy	(N, G) float32	adjusted p-value, 1 where untested
tested.npy	(N, G) bool	whether the gene was tested for the pair
lfc_true.npy	(N, G) float64	log2 fold change, NaN where untested
delta_p.npy	(N, G) float32	pseudobulk log1p expression of perturbed cells minus control mean
ctrl_means.npy	(C, G) float32	mean log1p expression of control cells per cell line
ctx_ids.npy	(N,) int32	cell line of each row, index into context_to_id
pert_ids.npy	(N,) int32	perturbation of each row, index into pert_to_id

Usage

The replogle_wdataset and replogle_xdataset experiment configs pin this repo by commit, so pie train and pie eval download preprocessed/ automatically. In your own config, use hf://datasets/arcinstitute/PIE_replogle_nadig_essential@<commit>/preprocessed in data.preprocessed_dirs, or download a copy:

hf download arcinstitute/PIE_replogle_nadig_essential --repo-type dataset \
  --local-dir "$PIE_DATA_ROOT/replogle"