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ReUseData

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

Reusable and reproducible Data Management


Bioconductor version: Development (3.19)

ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".

Author: Qian Liu [aut, cre]

Maintainer: Qian Liu <qian.liu at roswellpark.org>

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

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("ReUseData")

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("ReUseData")
ReUseDataData HTML R Script
ReUseDataQS HTML R Script
ReUseDataRecipes HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, ImmunoOncology, Infrastructure, Preprocessing, Software
Version 1.3.2
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends
Imports Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk
System Requirements
URL https://github.com/rworkflow/ReUseData
Bug Reports https://github.com/rworkflow/ReUseData/issues
See More
Suggests knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ReUseData_1.3.2.tar.gz
Windows Binary
macOS Binary (x86_64) ReUseData_1.3.2.tgz
macOS Binary (arm64) ReUseData_1.3.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/ReUseData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReUseData
Bioc Package Browser https://code.bioconductor.org/browse/ReUseData/
Package Short Url https://bioconductor.org/packages/ReUseData/
Package Downloads Report Download Stats