ATAC-seq data analysis bioinformatics software tools

ATAC-seq allows simultaneous interrogation of factor occupancy, nucleosome positions in regulatory sites, and chromatin accessibility genome wide by considering the position of insertion and the distribution of insert lengths captured during the transposition reaction. Source…

ATAC-seq analysis steps

ATAC-seq data analysis bioinformatics software tools

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ALTRE
Web
Desktop

ALTRE ALTered Regulatory Elements

An R package and associated R Shiny web app for differential analysis of…

An R package and associated R Shiny web app for differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq or ATAC-seq. Users can run the workflow…

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DeFCoM
Desktop

DeFCoM Detecting Footprints Containing Motifs

A supervised learning based footprint prediction framework. DeFCoM was designed…

A supervised learning based footprint prediction framework. DeFCoM was designed to capture variation in DNaseI signal within active footprints and unbound motif sites to enhance footprint…

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chromVAR
Desktop

chromVAR chromatin Variability

Analyses sparse chromatin accessibility data. chromVAR estimates the gain or…

Analyses sparse chromatin accessibility data. chromVAR estimates the gain or loss of accessibility within sets of peaks sharing the same motif or annotation while controlling for known technical…

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ATACseqQC
Desktop

ATACseqQC Assay for Transposase-Accessible Chromatin sequencing Quality Control

Allows to make chromatin accessibility analysis. ATACseqQC represents an…

Allows to make chromatin accessibility analysis. ATACseqQC represents an alternative tool to MNase-seq, FAIRE-seq and DNAse-seq. It helps users to quickly assess their ATAC-seq experiment. Comparing…

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ImpulseDE2
Desktop

ImpulseDE2

Corrects batch effects (from multiple confounding variables) and library depth.…

Corrects batch effects (from multiple confounding variables) and library depth. ImpulseDE2 is a differential expression algorithm for longitudinal count data sets which arise in sequencing…

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