MACS -- Model-based Analysis of ChIP-Seq

ATAC-seq and DNase-seq processing pipeline

chromatin Variability Across Regions (of the genome!)

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

deepStats: a stastitical toolbox for deeptools and genomic signals

Big data Regression for predicting DNase I hypersensitivity

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

CWL tools and workflows for GGR

Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility

Improving the feature density based peak caller with dynamic statistics

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

A robust statistical test for TF footprint data analyses

Refining TRE regions from dREG by imputing DHS.

This repository contains the prebuilt models for BIRD.

A dataset for big data prediction.

Scripts to run footprinting and motif-flanking accessibility analysis in DNase-seq/ ATAC-seq data

Codes for data processing and figure generation