Package: ReUseData 1.13.1

Qian Liu

ReUseData: Reusable and reproducible Data Management

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()".

Authors:Qian Liu [aut, cre]

ReUseData_1.13.1.tar.gz
ReUseData_1.13.1.zip(r-4.7)ReUseData_1.13.1.zip(r-4.6)ReUseData_1.13.1.zip(r-4.5)
ReUseData_1.13.1.tgz(r-4.6-any)ReUseData_1.13.1.tgz(r-4.5-any)
ReUseData_1.13.1.tar.gz(r-4.7-any)ReUseData_1.13.1.tar.gz(r-4.6-any)
ReUseData_1.13.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ReUseData/json (API)

# Install 'ReUseData' in R:
install.packages('ReUseData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rworkflow/reusedata/issues

On BioConductor:ReUseData-1.13.1(bioc 3.24)ReUseData-1.12.0(bioc 3.23)

softwareinfrastructuredataimportpreprocessingimmunooncology

5.56 score 4 stars 8 scripts 22 exports 113 dependencies

Last updated from:8d2f1ee0dd. Checks:4 ERROR, 4 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR231
linux-devel-x86_64NOTE1154
source / vignettesOK1018
linux-release-x86_64NOTE1137
macos-release-arm64NOTE517
macos-oldrel-arm64NOTE594
windows-develERROR258
windows-releaseERROR287
windows-oldrelERROR247
wasm-releaseOK181

Exports:annDatadataHubdataNamesdataNotesdataParamsdataPathsdataSearchdataTagsdataTags<-dataUpdatedataYmlgetCloudDatagetDatameta_datarecipeHubrecipeLoadrecipeMakerecipeNamesrecipeSearchrecipeUpdateshowtoList

Dependencies:askpassbackportsbase64encbase64urlbasiliskbatchtoolsBHBiocFileCacheBiocGenericsBiocParallelbitbit64blobbrewbslibcachemcheckmateclicliprcodetoolscommonmarkcpp11crayoncurldata.tableDBIdbplyrDiagrammeRdigestdir.expirydplyrevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsgit2rglueherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphjquerylibjsonliteknitrlabelinglambda.rlaterlatticelifecyclemagrittrMatrixmemoisemimeopensslotelpillarpkgconfigpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLRcwlRcwlPipelinesreadrreticulaterlangrmarkdownrprojrootRSQLiterstudioapiS4Vectorssassscalesshinysnowsourcetoolsstringistringrsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunxtableyaml

ReUseData: Reusable and Reproducible Data Management
Installation | ReUseData core functions for data management | Data generation | Data caching, updating and searching | Existing data annotation | Cloud data resources | Know your data | SessionInfo
Rendered fromReUseData_data.Rmdusingknitr::rmarkdown

Last update: 2023-11-14
Started: 2022-11-29

ReUseData: Reusable and Reproducible Data Management - quick start
Introduction | Package installation and loading | Data recipes | Search and load a data recipe | Evaluate a data recipe | Create your own data recipes | Reusable data | Update data files that are generated using ReUseData | Export data into workflow-ready files | Download pregenerated data from Google Cloud | SessionInfo
Rendered fromReUseData_quickStart.Rmdusingknitr::rmarkdown

Last update: 2023-11-14
Started: 2023-02-03

ReUseData: Workflow-based Data Recipes for Management of Reusable and Reproducible Data Resources
Introduction | Installation | Project resources | ReUseData recipe landing pages | ReUseData recipe scripts | ReUseData core functions | Recipe construction and evaluation | Recipe caching and updating | Recipe searching and loading | SessionInfo
Rendered fromReUseData_recipe.Rmdusingknitr::rmarkdown

Last update: 2023-11-14
Started: 2022-11-29

Readme and manuals

Help Manual

Help pageTopics
annDataannData
dataHub Classc,dataHub-method dataHub dataNames dataNotes dataParams dataPaths dataTags dataTags,dataHub-method dataTags<- dataTags<-,dataHub-method dataYml show,dataHub-method toList [,dataHub,ANY,ANY,ANY-method [<-,dataHub,ANY,ANY,ANY-method
dataSearch search data in local data caching systemdataSearch
dataUpdatedataUpdate
getCloudData Download the pregenerated curated data sets from ReUseData cloud bucketgetCloudData
getDatagetData
meta_datameta_data
recipeHubrecipeHub recipeNames show,recipeHub-method [,recipeHub,ANY,ANY,ANY-method
recipeLoadrecipeLoad
recipeMakerecipeMake
recipeSearchrecipeSearch
recipeUpdaterecipeUpdate
ReUseDataReUseData