BIT: Bayesian Identification of Transcriptional Regulators from Epigenomics-Based Query Region Sets

Data used for Project: "BIT: Bayesian Identification of Transcriptional Regulators from Epigenomics-Based Query Region Sets"

BIT package is available on GitHub: GitHub

We also provide a online web portal: BIT Portal

Please consult the manual for instructions on loading the reference data.

Please note that the preprocessed reference database must be pre-loaded before running function in BIT!!

File Description:

hg38_200.tar.gz: Pre-processed TR ChIP-seq reference datasets for genome hg38 with bin width 200.

hg38_500.tar.gz: Pre-processed TR ChIP-seq reference datasets for genome hg38 with bin width 500.

hg38_1000.tar.gz: Pre-processed TR ChIP-seq reference datasets for genome hg38 with bin width 1000.

mm10_200.tar.gz: Pre-processed TR ChIP-seq reference datasets for genome mm10 with bin width 200.

mm10_500.tar.gz: Pre-processed TR ChIP-seq reference datasets for genome mm10 with bin width 500.

mm10_1000.tar.gz: Pre-processed TR ChIP-seq reference datasets for genome mm10 with bin width 1000.

Input_Data.tar.gz: contains the input data for the four application cases, including differentially accessible regions (DARs) from bulk and single-cell perturbation experiments,  cancer-type-specific accessible regions, and cell-type-specific accessible regions.

Figure_Data_v2.tar.gz: is the updated figure data folder, which includes the data used to generate the manuscript’s plots, as well as the output from the benchmarking methods.

Figure.R: R code to replicate the figures, used together with Figure_Data_v2.tar.gz.

Depmap data can be accessed on DepMap Consortium: DepMap