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https://github.com/bioconductor-source/systempiperdata

https://github.com/bioconductor-source/systempiperdata

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: TeX
  • Default Branch: devel
  • Size: 463 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.md

systemPipeRdata: Workflow templates and sample data

platforms rank posts build updated dependencies

R-CMD-check

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, ChIP-Seq, VAR-Seq, Ribo-Seq and many others.

Installation

To install the package, please use the BiocManager::install command: if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("systemPipeRdata")

To obtain the most recent updates immediately, one can install it directly from github as follow: if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("tgirke/systemPipeRdata", build_vignettes=TRUE, dependencies=TRUE)

Due to the large size of the sample data (~320 MB) provided by systemPipeRdata, its download/install may take some time.

To install the parent package systemPipeR itself, please use the BiocManager::install method as instructed here.

Usage

Detailed user manuals are available here:

Additional information can be found on the corresponding Bioconductor packages.

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

.github/workflows/actions.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • ad-m/github-push-action master composite
  • peter-evans/repository-dispatch v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/update_cwl.yaml actions
  • actions/checkout v2 composite
  • ad-m/github-push-action master composite
DESCRIPTION cran
  • R >= 3.6.0 depends
  • BiocGenerics * imports
  • Biostrings * imports
  • jsonlite * imports
  • methods * imports
  • remotes * imports
  • BiocStyle * suggests
  • GenomicFeatures * suggests
  • GenomicRanges * suggests
  • IRanges * suggests
  • RUnit * suggests
  • Rsamtools * suggests
  • ShortRead * suggests
  • dplyr * suggests
  • kableExtra * suggests
  • knitr * suggests
  • magrittr * suggests
  • rmarkdown * suggests
  • rtracklayer * suggests
  • systemPipeR * suggests