systemPipeRdata
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata.
systemPipeRdata: Workflow templates and sample data
Bioconductor version: 3.13
systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR's overview vignette.
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke at ucr.edu>
citation("systemPipeRdata")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("systemPipeRdata")
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("systemPipeRdata")| systemPipeRdata: Workflow templates and sample data | HTML | R Script |
| WF: ChIP-Seq Workflow Template | HTML | R Script |
| WF: RIBO-Seq Workflow Template | HTML | R Script |
| WF: RNA-Seq Workflow Template | HTML | R Script |
| WF: VAR-Seq Template | HTML | R Script |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep |
| Version | 1.20.0 |
| License | Artistic-2.0 |
| Depends | methods |
| Imports | BiocGenerics, jsonlite, remotes, GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer |
| System Requirements | |
| URL | https://github.com/tgirke/systemPipeRdata |
See More
| Suggests | RUnit, BiocStyle, knitr, rmarkdown, systemPipeR |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | RNASeqR |
| Suggests Me | systemPipeR, systemPipeShiny |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | systemPipeRdata_1.20.0.tar.gz |
| Windows Binary | |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/systemPipeRdata |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/systemPipeRdata |
| Package Short Url | https://bioconductor.org/packages/systemPipeRdata/ |
| Package Downloads Report | Download Stats |