- Home
- Bioconductor 3.4
- Software Packages
- 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")
In most cases, you don't need to download the package archive at all.
systemPipeR
|
|
|
|
|
|
|
|
systemPipeR: NGS workflow and report generation environment
Bioconductor version: Release (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")
| R Script | ChIP-Seq Workflow Template | |
| R Script | Ribo-Seq Workflow Template | |
| R Script | RNA-Seq Workflow Template | |
| R Script | VAR-Seq Workflow Template | |
| HTML | R Script | Overview Vignette |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | systemPipeR_1.8.1.tar.gz |
| Windows Binary | systemPipeR_1.8.1.zip |
| Mac OS X 10.9 (Mavericks) | systemPipeR_1.8.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/systemPipeR/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/systemPipeR/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
