dnase-seq topic

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

slowkow

MACS -- Model-based Analysis of ChIP-Seq

macs3-project

ATAC-seq and DNase-seq processing pipeline

kundajelab

chromatin Variability Across Regions (of the genome!)

GreenleafLab

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

CostaLab

deepStats: a stastitical toolbox for deeptools and genomic signals

gtrichard

Big data Regression for predicting DNase I hypersensitivity

WeiqiangZhou

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

SUwonglab

CWL tools and workflows for GGR

Duke-GCB