systemPipeR

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeR.

systemPipeR: NGS workflow and report generation environment


Bioconductor version: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("systemPipeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("systemPipeR")
ChIP-Seq Workflow Template HTML R Script
RIBO-Seq Workflow Template HTML R Script
RNA-Seq Workflow Template HTML R Script
systemPipeR: NGS workflow and report generation environment HTML R Script
VAR-Seq Workflow Template HTML R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, Software
Version 1.18.2
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends Rsamtools(>= 1.31.2), Biostrings, ShortRead(>= 1.37.1), methods
Imports BiocGenerics, GenomicRanges, GenomicFeatures(>= 1.31.3), SummarizedExperiment, VariantAnnotation(>= 1.25.11), rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, batchtools, yaml
System Requirements 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.
URL http://tgirke.github.io/systemPipeR
See More
Suggests ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager
Linking To
Enhances
Depends On Me
Imports Me DiffBind, RNASeqR
Suggests Me systemPipeRdata
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package systemPipeR_1.18.2.tar.gz
Windows Binary systemPipeR_1.18.2.zip
Mac OS X 10.11 (El Capitan) systemPipeR_1.18.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/systemPipeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/systemPipeR
Bioc Package Browser https://code.bioconductor.org/browse/systemPipeR/
Package Short Url https://bioconductor.org/packages/systemPipeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive