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.
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Bioconductor version: 3.2
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("systemPipeR")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("systemPipeR")
ChIP-Seq Workflow Template | ||
Ribo-Seq Workflow Template | ||
RNA-Seq Workflow Template | ||
VAR-Seq Workflow Template | ||
HTML | Overview Vignette | |
Reference Manual | ||
Text | README | |
Text | NEWS |
biocViews | Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, Software |
Version | 1.4.8 |
In Bioconductor since | BioC 3.0 (R-3.1) (1.5 years) |
License | Artistic-2.0 |
Depends | Rsamtools, Biostrings, ShortRead, methods |
Imports | BiocGenerics, GenomicRanges, GenomicFeatures, SummarizedExperiment, VariantAnnotation, rjson, grid, ggplot2, 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 |
Follow Installation instructions to use this package in your R session.
Package Source | systemPipeR_1.4.8.tar.gz |
Windows Binary | systemPipeR_1.4.8.zip |
Mac OS X 10.6 (Snow Leopard) | systemPipeR_1.4.4.tgz |
Mac OS X 10.9 (Mavericks) | systemPipeR_1.4.8.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/systemPipeR/tree/release-3.2 |
Package Short Url | http://bioconductor.org/packages/systemPipeR/ |
Package Downloads Report | Download Stats |
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