ReUseData

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

Reusable and reproducible Data Management

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-1456-5099

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

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

Qian Liu. ReUseData: Reusable and reproducible Data Management. doi:10.18129/B9.bioc.ReUseData, R package version 1.13.1, https://bioconductor.org/packages/ReUseData.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, ImmunoOncology, Infrastructure, Preprocessing, Software
Version	1.13.1
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 years)
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

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, r-universe

Package Archives

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

Source Package	ReUseData_1.13.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	ReUseData_1.13.1.tgz
macOS Binary (sonoma-arm64)	ReUseData_1.13.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ReUseData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ReUseData
Package Short Url	https://bioconductor.org/packages/ReUseData/
Package Downloads Report	Download Stats