# Chem-PerturBridge DEG Outputs

Differential gene expression `.h5ad` outputs for Chem-PerturBridge datasets whose upstream terms allow redistribution.

The files are staged under `<dataset>/group_rep/` and `<dataset>/sep_rep/`. Each file corresponds to one cell line or context.

## License

The collection curation and packaging are released under CC BY 4.0.

CC BY 4.0 for Chem-PerturBridge curation/packaging; preserve each upstream license, notice, and attribution.

Each upstream dataset retains its original license, attribution, and notice requirements. See `dge_upload_manifest.tsv` for per-file provenance.

## Files

- `l1000_phase1/sep_rep/`: 70 files
- `l1000_phase2/sep_rep/`: 30 files
- `novartis_batch_2500/sep_rep/`: 1 file
- `op3/sep_rep/`: 4 files
- `sciplex/sep_rep/`: 3 files
- `tahoe/sep_rep/`: 48 files
- `vcpi_0001/sep_rep/`: 1 file
- `vcpi_0002/sep_rep/`: 1 file

## Sources And Notices

- `l1000_phase1`: LINCS L1000 Phase I, GEO GSE92742 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742. Cite LINCS L1000/GSE92742 and preserve upstream attribution.
- `l1000_phase2`: LINCS L1000 Phase II, GEO GSE70138 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138. Cite LINCS L1000/GSE70138 and preserve upstream attribution.
- `novartis_batch_2500`: Novartis DRUG-seq U2OS MoABox Dataset - https://zenodo.org/records/14291446. Retain the Novartis/Zenodo MIT license notice and citation.
- `op3`: OP3 perturbation prediction dataset, GEO GSE279945 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279945. Cite OP3/Open Problems and GSE279945.
- `sciplex`: scPerturb / SrivatsanTrapnell2020_sciplex3 - https://zenodo.org/records/13350497. Cite scPerturb/Sci-Plex and include CC BY 4.0 attribution.
- `tahoe`: Tahoe-100M - https://huggingface.co/datasets/tahoebio/Tahoe-100M. Citation requested by the dataset card; attribution still recommended.
- `vcpi_0001`: Virtual Cell Pharmacology Initiative public release - https://thevirtualcell.com/. Cite VCPI/Ginkgo Datapoints and include CC BY 4.0 attribution.
- `vcpi_0002`: Virtual Cell Pharmacology Initiative public release - https://thevirtualcell.com/. Cite VCPI/Ginkgo Datapoints and include CC BY 4.0 attribution.