systemPipeR

DOI: 10.18129/B9.bioc.systemPipeR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see systemPipeR.

systemPipeR: NGS workflow and report generation environment

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	systemPipeR and CWL
HTML	R Script	systemPipeR: Workflow design and reporting generation environment
HTML	R Script	systemPipeR: Workflows collection
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, ReportWriting, RiboSeq, SNP, Sequencing, Software, Workflow
Version	1.26.3
In Bioconductor since	BioC 3.0 (R-3.1) (7 years)
License	Artistic-2.0
Depends	Rsamtools(>= 1.31.2), Biostrings, ShortRead(>= 1.37.1), methods
Imports	GenomicRanges, GenomicFeatures(>= 1.31.3), SummarizedExperiment, VariantAnnotation(>= 1.25.11), rjson, ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, batchtools, yaml, stringr, assertthat, magrittr, DOT, rsvg, IRanges, testthat, S4Vectors, crayon
LinkingTo
Suggests	BiocGenerics, ape, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager, systemPipeRdata, GenomicAlignments, grid, DT, dplyr, kableExtra
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://systempipe.org/
Depends On Me
Imports Me	DiffBind, RNASeqR
Suggests Me	systemPipeRdata, systemPipeShiny, systemPipeTools
Links To Me
Build Report

Package Archives

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

Source Package	systemPipeR_1.26.3.tar.gz
Windows Binary	systemPipeR_1.26.3.zip
macOS 10.13 (High Sierra)	systemPipeR_1.26.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/systemPipeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/systemPipeR
Package Short Url	https://bioconductor.org/packages/systemPipeR/
Package Downloads Report	Download Stats