README.md

---
license: other
language:
- en
tags:
- single-cell
- perturb-seq
- base-editing
- scSNV-seq
- virtual-cell
pretty_name: PertResolve-Bench datasets
---

# PertResolve-Bench datasets

This repository contains the allele-resolved data and the public perturbation
datasets used by the PertResolve manuscript. It is a data release only: it
does not contain the manuscript figures, analysis code, model predictions, or
the `results/` directory. The corresponding code and result reports remain in
the [PertResolve GitHub repository](https://github.com/Boom5426/PertResolve).

## Included data

### Allele-resolved benchmark

- `benchmark/allele_perturb_bench.csv`: 470 protein-coding variant conditions
  plus two wild-type reference rows, with gene, protein, biophysical features,
  cell counts and evaluation partitions.
- `benchmark/hotspot_external_definition.txt`: external hotspot definition
  used by the benchmark annotations.
- `benchmark/supplementary_data_1_datasets.xlsx`: the Supplementary Data 1
  inventory and source metadata.

The complete compact allele package is included:

- **TP53 and KRAS (GSE161824):** processed cell-by-gene matrices, cell and
  gene tables, cell metadata and `variants2cell` assignments under
  `allele/ursu_gse161824/`. Source: [GEO GSE161824](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161824).
- **GATA1 (GSE215253/PerturbNet processing):**
  `allele/gata1/GATA1_standard_hvg_pert_filtered.h5ad`, variant and theta
  tables, and the processed array under `allele/gata1_arrays.npz`. Source:
  [GEO GSE215253](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215253)
  and the [PerturbNet repository](https://github.com/cyclopeta/PerturbNet_reproduce).
- **JAK1 (scSNV-seq):** the genotyped single-cell object
  `allele/jak1/sce_genotyped.rds`, cell/gene/experiment metadata, theta table
  and `allele/jak1_arrays.npz`. Sources: [ENA PRJEB48915](https://www.ebi.ac.uk/ena/browser/view/PRJEB48915)
  and [Zenodo record 10418435](https://zenodo.org/records/10418435).
- `allele/joint_arrays.npz`, `allele/real_deltas.npz` and
  `allele/barcode_rebuild_provenance.json`: compact processed products and
  provenance for the allele analyses.
- `allele/esm1v_embeddings.npz`: ESM-1v variant embeddings used as molecular
  features. Model weights are not redistributed; cite and follow the terms of
  [FAIR ESM](https://github.com/facebookresearch/esm) and Meier et al. (2021).

### Broader perturbation panel

The following paper-used resources are included when their complete source
resource is below the 100 GB release threshold:

- `external/scperturb/`: selected scPerturb h5ad objects for Norman,
  Replogle K562 essential, Adamson, McFarland, Frangieh RNA/protein, Papalexi
  ECCITE RNA/protein and sciPlex3, together with the source manifest. Source:
  [scPerturb Zenodo record 10044268](https://zenodo.org/records/10044268).
- `external/vcc/adata_Training.h5ad` and its small validation/gene-name tables:
  the VCC training object used in the paper. Source: [Arc Virtual Cell Atlas](https://virtualcellatlas.org/)
  and the associated Cell paper (DOI [10.1016/j.cell.2025.06.008](https://doi.org/10.1016/j.cell.2025.06.008)).
- `external/gse306429/`: the combined demultiplexed single-cell object and
  processed score/pseudobulk objects from GSE306429. Source: [GEO GSE306429](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE306429).
- `external/perturbmulti/`: processed CRISPR RNA and protein objects and the
  source README for PerturbMulti. Source: [GEO GSE275483](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE275483);
  the source README identifies the processed release as CC BY 4.0.

Files are stored in their native spaces. No `results/` tables, differential-
expression result objects, model checkpoints, prediction arrays, figures or
analysis scripts are included.

## Deliberate exclusions

Resources whose complete source resource exceeds 100 GB are not mirrored in
this repository. Their provenance is retained here so that they can be
retrieved from the original providers:

- [Tahoe-100M](https://huggingface.co/datasets/tahoebio/Tahoe-100M) full h5ad
  collection (about 320 GB),
- [X-Atlas/Orion](https://huggingface.co/datasets/Xaira-Therapeutics/X-Atlas-Orion)
  (about 118 GB),
- the KOLF pan-genome object (about 234 GB; see the [Arc Virtual Cell Atlas
  release](https://virtualcellatlas.org/)), and
- the Parse 10M PBMC object (about 212 GB; source/hosting details are given in
  the PertResolve manuscript and its preregistration).

The protocol-excluded non-cell-level CIGS and cpg0016 resources are also not
included. These exclusions do not remove the corresponding benchmark
definitions from the manuscript; they only avoid redistributing very large or
out-of-scope source resources.

## Provenance, licensing and citation

The Hugging Face repository is marked `license: other` because it combines
author-generated annotations/derived products with files derived from public
third-party datasets. This label is intentional and is not an Apache-2.0 grant
for the third-party files. The original provider terms and attribution
requirements apply to each source dataset; see `NOTICE`, the source manifests
and per-resource source notes. The benchmark metadata and provenance text
written for this release may be reused with attribution to the PertResolve
authors, but no underlying third-party data are relicensed.

Please cite the PertResolve manuscript and the original source records listed
above when using these data. `MANIFEST.sha256` records the checksum of every
included data or metadata file.