recipe bioconductor-esatac

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.



GPL-3 | file LICENSE



package bioconductor-esatac

(downloads) docker_bioconductor-esatac


1.4.3-0, 1.4.0-0

Depends bioconductor-annotationdbi


Depends bioconductor-biocgenerics


Depends bioconductor-biostrings


Depends bioconductor-bsgenome


Depends bioconductor-chipseeker


Depends bioconductor-clusterprofiler


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicfeatures


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-jaspar2016


Depends bioconductor-motifmatchr


Depends bioconductor-rbowtie2


Depends bioconductor-rsamtools


Depends bioconductor-rtracklayer


Depends bioconductor-s4vectors


Depends bioconductor-shortread


Depends bioconductor-tfbstools


Depends libgcc-ng


Depends libstdcxx-ng


Depends r-base


Depends r-biocmanager

Depends r-corrplot

Depends r-diagrammer

Depends r-digest

Depends r-ggplot2

Depends r-igraph

Depends r-knitr

Depends r-magrittr

Depends r-r.utils

Depends r-rcpp


Depends r-rjava

Depends r-rmarkdown

Depends r-venndiagram



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-esatac

and update with:

conda update bioconductor-esatac

or use the docker container:

docker pull<tag>

(see bioconductor-esatac/tags for valid values for <tag>)