"Title","Description","BiocVersion","Genome","SourceType","SourceUrl","SourceVersion","Species","TaxonomyId","Coordinate_1_based","DataProvider","Maintainer","RDataClass","DispatchClass","RDataPath"
"Response of prostate cancer cells to drug treatment","Gene expression and ATACseq data from 6 cell lines (LNCaP, VCaP, MDA, 22Rv1, DU145, H660) after treatment with AR-targeting drugs","3.20","hg38","HDF5","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE251977","Sep 09 2024","Homo sapiens","9606",TRUE,"Genentech, Inc.","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/AR_drug.h5"
"Single-cell analysis of samples from healthy human colon","ATACseq and RNAseq data obtained by the colon tissues analysis. Samples were collected from adult human donors.","3.17","hg38","tar.gz","https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE165659&format=file","Feb 16 2021","Homo sapiens","9606",TRUE,"Stanford University","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/colonHealthy.h5"
"scATAC-seq and unpaired scRNA-seq of hematopoetic cells","Example scATAC-seq data of hematopoietic cells included in ArchR package was integrated with scRNAseq. ScATAC-seq data was obtained from GSE139369 and scRNA-seq obtained from https://jeffgranja.s3.amazonaws.com/ArchR/TestData/scRNA-Hematopoiesis-Granja-2019.rds","3.17","hg19","FASTQ","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139369","2019-10-29","Homo sapiens","9606",TRUE,"Stanford","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/hematopoiesis"
"PBMC Data Set","PBMC from a Healthy Donor - Granulocytes Removed Through Cell Sorting (10k)","3.20","hg38","HDF5","https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/","2021-05-03","Homo sapiens","9606",TRUE,"10X Genomics","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/PBMC_10x.h5"
"LNCaP Cells Treated with Enzalutamide","Multiome data (scATAC and scRNAseq) for enzalutamide-treated LNCaP cells. Measured (unpaired) with Illumina NextSeq 500 (GPL18573). Results stored in GEO, acc.nos: GSE168667 and GSE168668.","3.17","hg38","tar.gz","https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE168667&format=file, https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE168668&format=file","Sep 08 2021","Homo sapiens","9606",TRUE,"Tampere University","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/prostateENZ.h5"
"Reprogram-seq of LNCaP cells","scMultiome data of LNCaP infected with FOXA1, NKX2-1, GATA6","3.17","hg38","HDF5","https://www.ncbi.nlm.nih.gov/geo/","2022-10-06","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/reprogramSeq.h5"
"Resistance of TEAD inhibitor to drug","Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition","3.20","hg38","HDF5","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE247442","2022-05-19","Homo sapiens","9606",TRUE,"Genentech, Inc.","Xiaosai Yao <xiaosai.yao@gmail.com>","MultiAssayExperiment","FilePath","scMultiome/TEADi_resistance.h5"
"TF Binding Info hg19 (ChIP-Atlas and ENCODE)","Combined transcription factor ChIP-seq data from ChIP-Atlas and ENCODE","3.17","hg19","BED","https://github.com/inutano/chip-atlas/","2021-09-21","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","GRangesList","FilePath","scMultiome/tfBinding_hg19_atlas.rds"
"TF Binding Info hg19 by sample (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by sample","3.19","hg19","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg19_atlas.sample.rds"
"TF Binding Info hg19 by sample (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by sample v2","3.21","hg19","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg19_atlas.sample_v2.rds"
"TF Binding Info hg19 by tissue (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by tissue","3.19","hg19","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg19_atlas.tissue.rds"
"TF Binding Info hg19 by tissue (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by tissue v2","3.21","hg19","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg19_atlas.tissue_v2.rds"
"TF Binding Info hg19 by sample (ENCODE)","Transcription factor ChIP-seq data from ENCODE broken down by sample","3.19","hg19","BED","https://www.encodeproject.org/","2021-09-21","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg19_encode.sample.rds"
"TF Binding Info hg19 by sample (ENCODE)","Transcription factor ChIP-seq data from ENCODE broken down by sample v2","3.21","hg19","BED","https://www.encodeproject.org/","2021-09-21","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg19_encode.sample_v2.rds"
"TF Binding Info hg38 (ChIP-Atlas and ENCODE)","Combined transcription factor ChIP-seq data from ChIP-Atlas and ENCODE","3.17","hg38","BED","https://github.com/inutano/chip-atlas/","2021-09-21","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","GRangesList","FilePath","scMultiome/tfBinding_hg38_atlas.rds"
"TF Binding Info hg38 by sample (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by sample","3.19","hg38","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg38_atlas.sample.rds"
"TF Binding Info hg38 by sample (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by sample v2","3.21","hg38","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg38_atlas.sample_v2.rds"
"TF Binding Info hg38 by tissue (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by tissue","3.19","hg38","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg38_atlas.tissue.rds"
"TF Binding Info hg38 by tissue (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by tissue v2","3.21","hg38","BED","https://github.com/inutano/chip-atlas/","3.0","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg38_atlas.tissue_v2.rds"
"TF Binding Info hg38 by sample (ENCODE)","Transcription factor ChIP-seq data from ENCODE broken down by sample","3.19","hg38","BED","https://www.encodeproject.org/","2021-09-21","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg38_encode.sample.rds"
"TF Binding Info hg38 by sample (ENCODE)","Transcription factor ChIP-seq data from ENCODE broken down by sample v2","3.21","hg38","BED","https://www.encodeproject.org/","2021-09-21","Homo sapiens","9606",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_hg38_encode.sample_v2.rds"
"TF Binding Info mm10 (ChIP-Atlas and ENCODE)","Combined transcription factor ChIP-seq data from ChIP-Atlas and ENCODE","3.17","mm10","BED","https://github.com/inutano/chip-atlas/","2021-09-21","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","GRangesList","FilePath","scMultiome/tfBinding_mm10_atlas.rds"
"TF Binding Info mm10 by sample (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by sample","3.19","mm10","BED","https://github.com/inutano/chip-atlas/","3.0","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_mm10_atlas.sample.rds"
"TF Binding Info mm10 by sample (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by sample v2","3.21","mm10","BED","https://github.com/inutano/chip-atlas/","3.0","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_mm10_atlas.sample_v2.rds"
"TF Binding Info mm10 by tissue (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by tissue","3.19","mm10","BED","https://github.com/inutano/chip-atlas/","3.0","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_mm10_atlas.tissue.rds"
"TF Binding Info mm10 by tissue (ChIP-Atlas)","Transcription factor ChIP-seq data from ChIP-Atlas broken down by tissue v2","3.21","mm10","BED","https://github.com/inutano/chip-atlas/","3.0","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_mm10_atlas.tissue_v2.rds"
"TF Binding Info mm10 by sample (ENCODE)","Transcription factor ChIP-seq data from ENCODE broken down by sample","3.19","mm10","BED","https://www.encodeproject.org/","2021-09-21","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_mm10_encode.sample.rds"
"TF Binding Info mm10 by sample (ENCODE)","Transcription factor ChIP-seq data from ENCODE broken down by sample v2","3.21","mm10","BED","https://www.encodeproject.org/","2021-09-21","Mus musculus","10090",TRUE,"Genentech","Xiaosai Yao <xiaosai.yao@gmail.com>","List","FilePath","scMultiome/tfBinding_mm10_encode.sample_v2.rds"
"TF motifs human","Transcription factor motifs in the human genome from chromVARmotifs package","3.19","","RDA","https://github.com/GreenleafLab/chromVARmotifs/raw/master/data/human_pwms_v2.rda","2","Homo sapiens","9606",NA,"Stanford University School of Medicine","Xiaosai Yao <xiaosai.yao@gmail.com>","PWMatrixList","FilePath","scMultiome/human_pwms_v2.rds"
"TF motifs mouse","Transcription factor motifs in the mouse genome from chromVARmotifs package","3.19","","RDA","https://github.com/GreenleafLab/chromVARmotifs/raw/master/data/human_pwms_v2.rda","2","Mus musculus","10090",NA,"Stanford University School of Medicine","Xiaosai Yao <xiaosai.yao@gmail.com>","PWMatrixList","FilePath","scMultiome/mouse_pwms_v2.rds"
