recipe bioconductor-systempiper

R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/systemPipeR.html

License

Artistic-2.0

Recipe

/bioconductor-systempiper/meta.yaml

Links

biotools: systempiper

package bioconductor-systempiper

Versions

1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.2-0, 1.9.0-0, 1.4.8-0, 1.4.7-0

Depends

• bioconductor-annotate >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-deseq2 >=1.22.0,<1.23.0

• bioconductor-edger >=3.24.0,<3.25.0

• bioconductor-genomicfeatures >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-go.db >=3.7.0,<3.8.0

• bioconductor-gostats >=2.48.0,<2.49.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-shortread >=1.40.0,<1.41.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• bioconductor-variantannotation >=1.28.0,<1.29.0

• r-base >=3.5.1,<3.5.2.0a0

• r-batchjobs

• r-ggplot2

• r-pheatmap

• r-rjson

Required By

• bioconductor-rnaseqr

• bioconductor-diffbind

Installation

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

conda install bioconductor-systempiper

and update with:

conda update bioconductor-systempiper

or use the docker container:

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

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

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-systempiper/README.html)