| access_date: "2026-06-04" |
| resources: |
| gasperini_crisprqtl: |
| purpose: "Primary S2T enhancer-gene benchmark." |
| status: "starter_files_downloaded_locally" |
| accession: "GEO:GSE120861" |
| coordinate_assembly: "hg19" |
| assembly_note: "At-scale enhancer coordinates are treated as hg19/GRCh37; chr1 coordinates exceeding GRCh38 length confirm the earlier hg38 assumption was unsafe." |
| publication_url: "https://pubmed.ncbi.nlm.nih.gov/30612741/" |
| geo_supplement_base_url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/" |
| files: |
| at_scale_pair_table: |
| url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/GSE120861_gene_gRNAgroup_pair_table.at_scale.txt.gz" |
| local_path: "data/raw/gasperini_gse120861/GSE120861_gene_gRNAgroup_pair_table.at_scale.txt.gz" |
| size_observed: "19M" |
| at_scale_deg_results: |
| url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/GSE120861_all_deg_results.at_scale.txt.gz" |
| local_path: "data/raw/gasperini_gse120861/GSE120861_all_deg_results.at_scale.txt.gz" |
| size_observed: "36M" |
| at_scale_grna_groups: |
| url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/GSE120861_grna_groups.at_scale.txt.gz" |
| local_path: "data/raw/gasperini_gse120861/GSE120861_grna_groups.at_scale.txt.gz" |
| size_observed: "128K" |
| license_or_terms: "Public GEO supplementary files; confirm redistribution policy before committing derived data." |
| arc_virtual_cell_challenge: |
| purpose: "Primary T2S gene perturbation response benchmark." |
| status: "manifested_not_downloaded_signature_builder_ready" |
| url: "https://github.com/ArcInstitute/arc-virtual-cell-atlas/blob/main/virtual-cell-challenge/README.md" |
| data_host: "Google Marketplace bucket" |
| bucket: "gs://arc-institute-virtual-cell-atlas/virtual-cell-challenge/" |
| coordinate_assembly: "not_applicable_single_cell_expression" |
| cell_context: "H1 hESC" |
| modality: "CRISPRi" |
| statistics: |
| cells: "~300,000" |
| target_genes: 300 |
| files: |
| training_h5ad: |
| url: "gs://arc-institute-virtual-cell-atlas/virtual-cell-challenge/2025/train/adata_Training.h5ad" |
| local_path: "data/raw/vcc/2025/train/adata_Training.h5ad" |
| training_perturbation_counts: |
| url: "gs://arc-institute-virtual-cell-atlas/virtual-cell-challenge/2025/train/pert_counts_Training.csv" |
| local_path: "data/raw/vcc/2025/train/pert_counts_Training.csv" |
| derived_outputs: |
| perturbation_signatures: |
| local_path: "data/processed/t2s/vcc_2025/perturbation_signatures.h5ad" |
| status: "builder_ready_pending_raw_download" |
| license_or_terms: "Follow Arc VCC and Google Marketplace dataset terms before downloading or redistributing derived signatures." |
| encode_ccre_screen: |
| purpose: "Regulatory annotations." |
| status: "PLS_and_ELS_lifted_to_hg19_and_annotated_gasperini" |
| url: "https://screen.wenglab.org/downloads" |
| version: "SCREEN Registry V4, Human GRCh38/hg38" |
| coordinate_assembly: "hg38" |
| assembly_note: "Do not use directly with the hg19 Gasperini benchmark. Use hg19 cCREs or liftOver with QC." |
| liftover: |
| target_assembly: "hg19" |
| config: "configs/ccre_liftover.yaml" |
| chain_url: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz" |
| local_chain_path: "data/raw/ucsc_liftover/hg38ToHg19.over.chain.gz" |
| bed_plus: 4 |
| status: "complete" |
| qc_yaml: "data/interim/screen_v4_liftover/hg19/liftover_qc.yaml" |
| lifted_records: |
| promoter_like: |
| input_records: 47532 |
| lifted_records: 47396 |
| lifted_fraction: 0.9971387696709585 |
| enhancer_like: |
| input_records: 1718669 |
| lifted_records: 1715351 |
| lifted_fraction: 0.9980694362905248 |
| derived_outputs: |
| gasperini_region_annotation: |
| qc_yaml: "data/processed/s2t/gasperini_gse120861/ccre_annotation_qc.yaml" |
| regions_with_ccre: 5810 |
| regions_total: 6143 |
| files: |
| promoter_like: |
| url: "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.PLS.bed" |
| local_path: "data/raw/screen_v4/GRCh38-cCREs.PLS.bed" |
| enhancer_like: |
| url: "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.ELS.bed" |
| local_path: "data/raw/screen_v4/GRCh38-cCREs.ELS.bed" |
| license_or_terms: "SCREEN download page requests citation of Moore...Weng (2026) Nature; confirm redistribution policy before committing derived annotations." |
| abc_maps: |
| purpose: "Enhancer-gene contact/activity prior." |
| status: "K562_filtered_predictions_downloaded_locally" |
| url: "https://www.engreitzlab.org/resources/" |
| coordinate_assembly: "hg19" |
| assembly_note: "Local K562 filtered file has chr1 intervals beyond GRCh38 length and aligns with hg19-coordinate Gasperini regions." |
| source_file: |
| url: "https://mitra.stanford.edu/engreitz/oak/public/Nasser2021/AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz" |
| size_observed: "324M" |
| local_filtered_file: "data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz" |
| filter: "header plus rows matching K562; observed CellType is K562-Roadmap" |
| license_or_terms: "Public Engreitz Lab resource; confirm redistribution policy before committing derived ABC scores." |
| encode_re2g: |
| purpose: "No-training external S2T field-model comparison." |
| status: "thresholded_k562_files_downloaded_lifted_and_scored" |
| url: "https://www.encodeproject.org/" |
| model_repo: "https://github.com/EngreitzLab/ENCODE_rE2G" |
| portal: "https://e2g.stanford.edu/" |
| coordinate_assembly: "GRCh38" |
| assembly_note: "Released ENCODE-rE2G files are GRCh38 and must be lifted to hg19 before joining to Gasperini." |
| config: "configs/external_e2g_sources.yaml" |
| liftover: |
| target_assembly: "hg19" |
| chain_url: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz" |
| local_chain_path: "data/raw/ucsc_liftover/hg38ToHg19.over.chain.gz" |
| bed_plus: 3 |
| qc_yaml: "data/external/external_e2g_liftover_qc.yaml" |
| files: |
| dnase_eot_thresholded: |
| accession: "ENCFF976OKL" |
| url: "https://www.encodeproject.org/files/ENCFF976OKL/" |
| download_url: "https://www.encodeproject.org/files/ENCFF976OKL/@@download/ENCFF976OKL.bed.gz" |
| local_path: "data/raw/external_e2g/encode_re2g/ENCFF976OKL.bed.gz" |
| lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF976OKL.hg19.bed" |
| output_type: "thresholded element gene links" |
| md5sum: "1989f02e1ed38c3831fca8abdfcf3d01" |
| extended_thresholded: |
| accession: "ENCFF269DKY" |
| url: "https://www.encodeproject.org/files/ENCFF269DKY/" |
| download_url: "https://www.encodeproject.org/files/ENCFF269DKY/@@download/ENCFF269DKY.bed.gz" |
| local_path: "data/raw/external_e2g/encode_re2g/ENCFF269DKY.bed.gz" |
| lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF269DKY.hg19.bed" |
| output_type: "thresholded element gene links" |
| md5sum: "c358ee5b33b4c03b2bef5ccf83e93c70" |
| dnase_eot_full: |
| accession: "ENCFF970QAX" |
| url: "https://www.encodeproject.org/files/ENCFF970QAX/" |
| download_url: "https://www.encodeproject.org/files/ENCFF970QAX/@@download/ENCFF970QAX.bed.gz" |
| local_path: "data/raw/external_e2g/encode_re2g/ENCFF970QAX.bed.gz" |
| lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF970QAX.hg19.bed" |
| output_type: "element gene links" |
| md5sum: "935d4418891babd748cd74dc074cf73f" |
| status: "downloaded_lifted_scored" |
| extended_full: |
| accession: "ENCFF950FTI" |
| url: "https://www.encodeproject.org/files/ENCFF950FTI/" |
| download_url: "https://www.encodeproject.org/files/ENCFF950FTI/@@download/ENCFF950FTI.bed.gz" |
| local_path: "data/raw/external_e2g/encode_re2g/ENCFF950FTI.bed.gz" |
| lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed" |
| output_type: "element gene links" |
| md5sum: "fd6affb3db931196ecd074e2ff46fc5f" |
| status: "downloaded_lifted_scored" |
| license_or_terms: "Released ENCODE files; cite ENCODE and ENCODE-rE2G. Use as external no-training comparisons unless terms are reviewed for training use." |
| jaspar: |
| purpose: "TF motif features and explanations." |
| status: "downloaded_locally_pilot_and_k562_erythroid_panel_scanned" |
| url: "https://jaspar.elixir.no/downloads" |
| release: "2026" |
| recommended_collection: "JASPAR CORE vertebrates non-redundant PFM" |
| pfm_url: "https://jaspar.elixir.no/download/data/2026/CORE/JASPAR2026_CORE_vertebrates_non-redundant_pfms_jaspar.txt" |
| local_pfm: "data/raw/jaspar/JASPAR2026_CORE_vertebrates_non-redundant_pfms_jaspar.txt" |
| sha256: "4005b5449ba07d9b58495f51143186e7e3959efd0ad670770fbddf57bf941e8f" |
| size_bytes: 336314 |
| derived_panels: |
| k562_erythroid_starter: |
| config: "configs/motif_panels/k562_erythroid.yaml" |
| n_motifs: 37 |
| output: "data/processed/s2t/gasperini_gse120861/sequence_features.jaspar2026_k562_erythroid.parquet" |
| feature_rows: 454582 |
| license_or_terms: "Open-access database; cite exact release and collection used." |
| ucsc_sequence_api: |
| purpose: "Lightweight hg19/hg38 region sequence extraction before motif scanning." |
| status: "used_for_gasperini_hg19_region_sequences" |
| url: "https://api.genome.ucsc.edu/getData/sequence" |
| local_cache_dir: "data/interim/ucsc_sequences" |
| license_or_terms: "UCSC Genome Browser API; cite UCSC Genome Browser where used." |
| alphagenome: |
| purpose: "No-training oracle/comparison only unless permission changes." |
| status: "optional_oracle" |
| url: "https://www.alphagenomedocs.com/index.html" |
| license_or_terms: "Do not train on API outputs under current conservative project rule." |
|
|
