systemPipeRdata

This is the released version of systemPipeRdata; for the devel version, see systemPipeRdata.

systemPipeRdata: Workflow templates and sample data

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DOI: 10.18129/B9.bioc.systemPipeRdata

Bioconductor version: Release (3.22)

systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.

Author: Thomas Girke

Maintainer: Thomas Girke <thomas.girke at ucr.edu>

Citation (from within R, enter citation("systemPipeRdata")):

Installation

To install this package, start R (version "4.5") 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: Basic Generic Template HTML R Script

WF: Basic Single Cell Template HTML R Script

WF: BLAST Template HTML R Script

WF: Cheminformatics Drug Similarity Template 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep

Version 2.14.0

License Artistic-2.0

Depends R (>= 3.6.0)

Imports methods, Biostrings, BiocGenerics, jsonlite, remotes

System Requirements

URL https://github.com/tgirke/systemPipeRdata

Suggests GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me systemPipeR, systemPipeShiny

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package systemPipeRdata_2.14.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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