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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")
In most cases, you don't need to download the package archive at all.
systemPipeR
systemPipeR: NGS workflow and report generation environment
Bioconductor version: 3.1
R package for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. An important feature is support for running command-line software, such as NGS aligners, on both single machines or compute clusters. 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 is not available
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")
| R Script | ChIP-Seq Report Template | |
| R Script | RNA-Seq Report Template | |
| R Script | VAR-Seq Report Template | |
| HTML | R Script | Overview Vignette |
| Reference Manual | ||
| Text | README |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing, Software |
| Version | 1.2.23 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1 year) |
| License | Artistic-2.0 |
| Depends | Rsamtools, Biostrings, ShortRead, methods |
| Imports | BiocGenerics, GenomicRanges, GenomicAlignments, VariantAnnotation, rjson, grid, ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs |
| LinkingTo | |
| Suggests | ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, GenomicFeatures, 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | systemPipeR_1.2.23.tar.gz |
| Windows Binary | systemPipeR_1.2.23.zip |
| Mac OS X 10.6 (Snow Leopard) | systemPipeR_1.2.23.tgz |
| Mac OS X 10.9 (Mavericks) | systemPipeR_1.2.23.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/systemPipeR/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/systemPipeR/ |
| Package Downloads Report | Download Stats |
Documentation »
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