dnase-seq

There are 1 repository under dnase-seq topic.

macs3-project / MACS
MACS -- Model-based Analysis of ChIP-Seq
chip-seq atac-seq dnase-seq peak-caller python poisson-equation macs
Language:Python 754
GreenleafLab / chromVAR
chromatin Variability Across Regions (of the genome!)
atac-seq bioinformatics dnase-seq r
Language:R 181
kundajelab / atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
atac-seq dnase-seq bioinformatics-pipeline
Language:Python 166
CostaLab / reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
atac-seq bioinformatics chip-seq differential-peak-calling dnase-seq footprinting genomics motif motif-analysis ngs
Language:Python 112
SUwonglab / PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
gene-regulatory-network gene-expression chromatin-accessibiity dnase-seq atac-seq rna-seq
Language:MATLAB 45
gtrichard / deepStats
deepStats: a stastitical toolbox for deeptools and genomic signals
deeptools galaxy genomic-signals genomics genomics-visualization bootstrap vizualize-data statistical-analysis dataviz sequencing chip-seq atac-seq dnase-seq rna-seq mnase-seq
Language:R 34
WeiqiangZhou / BIRD
Big data Regression for predicting DNase I hypersensitivity
rna-seq dnase-seq prediction-model single-cell-genomics gene-expression chromatin-accessibiity
Language:C++ 30
slowkow / CENTIPEDE.tutorial
:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
tutorial bioinformatics enrichment dnase-seq transcription-factors rstats
Language:R 26
Duke-GCB / GGR-cwl
CWL tools and workflows for GGR
atac-seq chip-seq cwl dnase-seq rna-seq
Language:Common Workflow Language 21
YosefLab / epitome
Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
chromatin-accessibility dnase-seq atac-seq epigenetic-events transcription-factors histone-modifications
Language:Python 10
Boyle-Lab / F-Seq2
Improving the feature density based peak caller with dynamic statistics
peak-caller dnase-seq chip-seq atac-seq kernel-density-estimation idr idr-analysis
Language:Python 7
durenzn / PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
atac-seq chromatin-accessibiity dnase-seq gene-expression gene-regulatory-network rna-seq
Language:MATLAB 4
Danko-Lab / dREG.HD
Refining TRE regions from dREG by imputing DHS.
dreg dnase-seq
Language:R 3
UcarLab / BiFET
A robust statistical test for TF footprint data analyses
atac-seq bioconductor chromatin-accessibiity dnase-seq footprinting r statistical-tests transcription-factor-binding
Language:R 2
WeiqiangZhou / BIRD-model
This repository contains the prebuilt models for BIRD.
rna-seq dnase-seq atac-seq prediction-model gene-expression
2
pmb59 / bivariate-genomic-footprinting
Scripts to run footprinting and motif-flanking accessibility analysis in DNase-seq/ ATAC-seq data
atac-seq footprinting dnase-seq
Language:R 1
WeiqiangZhou / BIRD-data
A dataset for big data prediction.
dnase-seq gene-expression microarray prediction-model genomics
1
rintukutum / TRF2-DNase-ChIP
Codes for data processing and figure generation
chip-seq computational-biology dnase-seq python r
Language:Python

dnase-seq

macs3-project / MACS

GreenleafLab / chromVAR

kundajelab / atac_dnase_pipelines

CostaLab / reg-gen

SUwonglab / PECA

gtrichard / deepStats

WeiqiangZhou / BIRD

slowkow / CENTIPEDE.tutorial

Duke-GCB / GGR-cwl

YosefLab / epitome

Boyle-Lab / F-Seq2

durenzn / PECA

Danko-Lab / dREG.HD

UcarLab / BiFET

WeiqiangZhou / BIRD-model

pmb59 / bivariate-genomic-footprinting

WeiqiangZhou / BIRD-data

rintukutum / TRF2-DNase-ChIP