ATAC-seq analysis steps

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 data analysis bioinformatics software tools

Web app
Desktop app
G T A T C G C T A ALTered Regulatory… ALTered Regulatory Elements

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…

Desktop app
G T A T C G C T A Detecting Footprints… Detecting Footprints Containing Motifs

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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