README_dge.md

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.