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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."
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