dnase-seq
There are 18 repositories under dnase-seq topic.
macs3-project/MACS
MACS -- Model-based Analysis of ChIP-Seq
kundajelab/atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
GreenleafLab/chromVAR
chromatin Variability Across Regions (of the genome!)
CostaLab/reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
SUwonglab/PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
gtrichard/deepStats
deepStats: a stastitical toolbox for deeptools and genomic signals
WeiqiangZhou/BIRD
Big data Regression for predicting DNase I hypersensitivity
slowkow/CENTIPEDE.tutorial
:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
Duke-GCB/GGR-cwl
CWL tools and workflows for GGR
YosefLab/epitome
Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
Boyle-Lab/F-Seq2
Improving the feature density based peak caller with dynamic statistics
durenzn/PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Danko-Lab/dREG.HD
Refining TRE regions from dREG by imputing DHS.
UcarLab/BiFET
A robust statistical test for TF footprint data analyses
WeiqiangZhou/BIRD-model
This repository contains the prebuilt models for BIRD.
pmb59/bivariate-genomic-footprinting
Scripts to run footprinting and motif-flanking accessibility analysis in DNase-seq/ ATAC-seq data
WeiqiangZhou/BIRD-data
A dataset for big data prediction.
rintukutum/TRF2-DNase-ChIP
Codes for data processing and figure generation