.. _`bioconductor-systempiper`:

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/release/bioc/html/systemPipeR.html
Versions 1.4.7
License  Artistic-2.0
Recipe   https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-systempiper
======== ===========

Installation
------------

.. highlight: bash

With an activated Bioconda channel (see :ref:`setup`), install with::

   conda install bioconductor-systempiper

and update with::

   conda update bioconductor-systempiper