MACS -- Model-based Analysis of ChIP-Seq

chromatin Variability Across Regions (of the genome!)

ATAC-seq and DNase-seq processing pipeline

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

Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling

Improving the feature density based peak caller with dynamic statistics

A unified framework for discovering, analyzing, integrating, and visualizing regulatory motifs and transcription factor binding sites across bulk, single-cell, and long-read sequencing modalities.

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

Refining TRE regions from dREG by imputing DHS.

This repository contains the prebuilt models for BIRD.

A robust statistical test for TF footprint data analyses

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

A dataset for big data prediction.

Codes for data processing and figure generation