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.
| Home | http://bioconductor.org/packages/3.6/bioc/html/systemPipeR.html |
| Versions | 1.10.2, 1.12.0, 1.4.7, 1.4.8, 1.9.0 |
| License | Artistic-2.0 |
| Recipe | https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-systempiper |
Installation¶
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-systempiper
and update with:
conda update bioconductor-systempiper
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-systempiper.
Link to this page¶
Render an 
badge with the following Markdown:
[](http://bioconda.github.io/recipes/bioconductor-systempiper/README.html)
