Package Recipe 'bioconductor-esatac'

recipe bioconductor-esatac

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

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/esATAC.html
License:: GPL-3 | file LICENSE
Recipe:: /bioconductor-esatac/meta.yaml
Links:: biotools: 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.

package bioconductor-esatac¶

Versions:

1.32.0-0, 1.24.0-1, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.20.0-0, 1.16.0-2, 1.16.0-1, 1.16.0-0,

1.32.0-0, 1.24.0-1, 1.24.0-0, 1.22.0-0, 1.20.0-1, 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:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0a0
on bioconductor-chipseeker >=1.46.0,<1.47.0
on bioconductor-chipseeker >=1.46.1,<1.47.0a0
on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-clusterprofiler >=4.18.4,<4.19.0a0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0a0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-jaspar2018 >=1.1.0,<1.2.0
on bioconductor-jaspar2018 >=1.1.1,<1.2.0a0
on bioconductor-motifmatchr >=1.32.0,<1.33.0
on bioconductor-motifmatchr >=1.32.0,<1.33.0a0
on bioconductor-pipeframe >=1.26.0,<1.27.0
on bioconductor-pipeframe >=1.26.0,<1.27.0a0
on bioconductor-rbowtie2 >=2.16.0,<2.17.0
on bioconductor-rbowtie2 >=2.16.0,<2.17.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on bioconductor-shortread >=1.68.0,<1.69.0
on bioconductor-shortread >=1.68.0,<1.69.0a0
on bioconductor-tfbstools >=1.48.0,<1.49.0
on bioconductor-tfbstools >=1.48.0,<1.49.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-biocmanager
on r-corrplot
on r-digest
on r-ggplot2
on r-igraph
on r-knitr
on r-magrittr
on r-r.utils
on r-rcpp >=0.12.11
on r-rjava
on r-rmarkdown
on r-venndiagram

Additional platforms:

linux-aarch64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-esatac

to add into an existing workspace instead, run:

pixi add bioconductor-esatac

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-esatac

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-esatac

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)