To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")

In most cases, you don't need to download the package archive at all.

systemPipeR

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see systemPipeR.

systemPipeR: NGS workflow and report generation environment

Bioconductor version: 3.4

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.

Author: Thomas Girke

Maintainer: Thomas Girke <thomas.girke at ucr.edu>

Citation (from within R, enter citation("systemPipeR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("systemPipeR")

PDF R Script ChIP-Seq Workflow Template

PDF R Script Ribo-Seq Workflow Template

PDF R Script RNA-Seq Workflow Template

PDF R Script VAR-Seq Workflow Template

HTML R Script Overview Vignette

PDF Reference Manual

Text README

Text NEWS

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, Software

Version 1.8.1

In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)

License Artistic-2.0

Depends Rsamtools, Biostrings, ShortRead, methods

Imports BiocGenerics, GenomicRanges, GenomicFeatures, SummarizedExperiment, VariantAnnotation, rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs

LinkingTo

Suggests ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel

SystemRequirements systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system.

Enhances

URL https://github.com/tgirke/systemPipeR

Depends On Me

Imports Me DiffBind

Suggests Me systemPipeRdata

Build Report