| # Chem-PerturBridge DEG Outputs |
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| Differential gene expression `.h5ad` outputs for Chem-PerturBridge datasets whose upstream terms allow redistribution. |
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| The files are staged under `<dataset>/group_rep/` and `<dataset>/sep_rep/`. Each file corresponds to one cell line or context. |
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| ## License |
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| The collection curation and packaging are released under CC BY 4.0. |
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| CC BY 4.0 for Chem-PerturBridge curation/packaging; preserve each upstream license, notice, and attribution. |
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| Each upstream dataset retains its original license, attribution, and notice requirements. See `dge_upload_manifest.tsv` for per-file provenance. |
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| ## Files |
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| - `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 |
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| ## Sources And Notices |
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| - `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. |
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