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To install this package, start R and enter:
source("http://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: 3.0
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 (PDF). 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:
source("http://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 | Overview Vignette | |
| R Script | RNA-Seq Report Template | |
| R Script | VAR-Seq Report Template | |
| Reference Manual | ||
| Text | README |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing, Software |
| Version | 1.0.12 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | Rsamtools, Biostrings, ShortRead, methods |
| Imports | BiocGenerics, rjson, grid, ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs |
| LinkingTo | |
| Suggests | ape, RUnit, BiocStyle, 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 | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | systemPipeR_1.0.12.tar.gz |
| Windows Binary | systemPipeR_1.0.12.zip |
| Mac OS X 10.6 (Snow Leopard) | systemPipeR_1.0.12.tgz |
| Mac OS X 10.9 (Mavericks) | systemPipeR_1.0.12.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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