systemPipeRdata

This is the development version of systemPipeRdata; for the stable release version, see systemPipeRdata.

systemPipeRdata: Workflow templates and sample data


Bioconductor version: Development (3.20)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep
Version 2.9.6
License Artistic-2.0
Depends R (>= 3.6.0)
Imports methods, Biostrings, BiocGenerics, jsonlite, remotes
System Requirements
URL https://github.com/tgirke/systemPipeRdata https://systempipe.org/
See More
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_2.9.6.tar.gz
Windows Binary
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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