recipe bioconductor-esatac

An Easy-to-use Systematic pipeline for ATACseq data analysis

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/esATAC.html

License:

GPL-3 | file LICENSE

Recipe:

/bioconductor-esatac/meta.yaml

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.

package bioconductor-esatac

Versions:

1.20.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.8.0-1,  1.6.1-0, 

1.20.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.8.0-1,  1.6.1-0,  1.4.3-0,  1.4.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-chipseeker >=1.34.0,<1.35.0

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-jaspar2018 >=1.1.0,<1.2.0

• bioconductor-motifmatchr >=1.20.0,<1.21.0

• bioconductor-pipeframe >=1.14.0,<1.15.0

• bioconductor-rbowtie2 >=2.4.0,<2.5.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-shortread >=1.56.0,<1.57.0

• bioconductor-tfbstools >=1.36.0,<1.37.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-biocmanager

• r-corrplot

• r-digest

• r-ggplot2

• r-igraph

• r-knitr

• r-magrittr

• r-r.utils

• r-rcpp >=0.12.11

• r-rjava

• r-rmarkdown

• r-venndiagram

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-esatac

and update with:

conda update bioconductor-esatac

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-esatac:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-esatac/README.html)