| --- |
| 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. |
|
|
