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."