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.







biotools: systempiper

package bioconductor-systempiper

(downloads) docker_bioconductor-systempiper


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


Depends bioconductor-biocgenerics


Depends bioconductor-biostrings


Depends bioconductor-deseq2


Depends bioconductor-edger


Depends bioconductor-genomicfeatures


Depends bioconductor-genomicranges


Depends bioconductor-go.db


Depends bioconductor-gostats


Depends bioconductor-limma


Depends bioconductor-rsamtools


Depends bioconductor-shortread


Depends bioconductor-summarizedexperiment


Depends bioconductor-variantannotation


Depends r-base


Depends r-batchjobs

Depends r-ggplot2

Depends r-pheatmap

Depends r-rjson



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<tag>

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