Single-cell Genomic Footprinting Benchmark

Data associated with the footprinting benchmark repository. ENCODE_snATAC.tar.gz ArchR project for the 11 ENCODE cell lines. singleFile_exampleOutput.tar.gz This is an example of what the raw footprinting output files for PRINT, HINT, and TOBIAS look like for one dataset (HEPG2, 5e6 reads, seed 21). Relates to the GitHub directory "scFootprintBenchmark/05_footprinting/03_reads/". baseline_cleaned_beds.tar.gz Footprinting bed files for the baseline ("original") samples. This is a common reference point for the jupyter notebooks. Relates to the GitHub directory "scFootprintBenchmark/06_dataquality/". 06_dataquality-{tool}-mats.tar.gz Standardized (OCR x PWM) matrices for all downsampling conditions for each program. Relates to the GitHub directory "scFootprintBenchmark/06_dataquality/". 07_cellsim-mats.tar.gz Standardized (OCR x PWM) matrices for all cell similarity sampling conditions for each program. Relates to the GitHub directory "scFootprintBenchmark/07_cellsim/". 11_chip-01_inputfiles.tar.gz Input files necessary to run the ChIP-to-footprinting comparison. Relates to the GitHub directory "scFootprintBenchmark/11_chip".