dnase-seq topic
CENTIPEDE.tutorial
:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
MACS
MACS -- Model-based Analysis of ChIP-Seq
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
chromVAR
chromatin Variability Across Regions (of the genome!)
reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
deepStats
deepStats: a stastitical toolbox for deeptools and genomic signals
BIRD
Big data Regression for predicting DNase I hypersensitivity
PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data