Package: BiocPkgTools 1.25.2

Sean Davis

BiocPkgTools: Collection of simple tools for learning about Bioconductor Packages

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

Authors:Shian Su [aut, ctb], Lori Shepherd [ctb], Marcel Ramos [aut, ctb], Felix G.M. Ernst [ctb], Jennifer Wokaty [ctb], Charlotte Soneson [ctb], Martin Morgan [ctb], Vince Carey [ctb], Sean Davis [aut, cre]

BiocPkgTools_1.25.2.tar.gz
BiocPkgTools_1.25.2.zip(r-4.5)BiocPkgTools_1.25.2.zip(r-4.4)BiocPkgTools_1.25.2.zip(r-4.3)
BiocPkgTools_1.25.2.tgz(r-4.4-any)BiocPkgTools_1.25.2.tgz(r-4.3-any)
BiocPkgTools_1.25.2.tar.gz(r-4.5-noble)BiocPkgTools_1.25.2.tar.gz(r-4.4-noble)
BiocPkgTools_1.25.2.tgz(r-4.4-emscripten)BiocPkgTools_1.25.2.tgz(r-4.3-emscripten)
BiocPkgTools.pdf |BiocPkgTools.html✨
BiocPkgTools/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/seandavi/biocpkgtools/issues

On BioConductor:BiocPkgTools-1.23.1(bioc 3.21)BiocPkgTools-1.24.0(bioc 3.20)

softwareinfrastructurebioconductormetadata

7.83 score 19 stars 69 scripts 468 downloads 1 mentions 46 exports 101 dependencies

Last updated 19 days agofrom:19ff67818c. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-winNOTENov 02 2024
R-4.5-linuxNOTENov 02 2024
R-4.4-winNOTENov 02 2024
R-4.4-macNOTENov 02 2024
R-4.3-winNOTENov 02 2024
R-4.3-macNOTENov 02 2024

Exports:activitySinceanacondaDownloadStatsbiocBuildEmailbiocBuildReportbiocBuildReportDBbiocBuildStatusDBbiocDownloadStatsbiocExplorebiocMaintainedbiocPkgListbiocPkgRangesbiocRevDepEmailbuildClassDepDatabuildClassDepFromPackagebuildClassDepGraphbuildPkgDependencyDataFramebuildPkgDependencyIgraphCRANstatusfirstInBiocget_bioc_dataget_cre_orcidsgetBiocVignettegetPackageInfogithubDetailsgithubURLPartshasBiocMaintinducedSubgraphByPkgslatestPkgStatsorcid_tablepkgBiocDepspkgBiocRevDepspkgCombDependencyGainpkgDepImportspkgDepMetricspkgDownloadRankpkgDownloadStatspkgToolsCacheplotClassDepplotClassDepDataplotClassDepGraphproblemPagerepositoryStatssentHistorysetCachesubgraphByDegreetemplatePath

Dependencies:askpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocManagerbiocViewsbitbit64bitopsblobbslibcachemclicliprcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdigestdplyrDTevaluatefansifastmapfauxpasfilelockfontawesomefsgenericsghgitcredsgluegraphhighrhmshtmltoolshtmlwidgetshttpcodehttpuvhttrhttr2igraphinijquerylibjsonliteknitrlaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrprettyunitsprogresspromisespurrrR6rappdirsRBGLRcppRCurlreadrrlangrmarkdownrorcidRSQLiteRUnitrvestsassselectrstringistringrsystibbletidyrtidyselecttinytextriebeardtzdburltoolsutf8vctrsvroomwhiskerwithrxfunXMLxml2yaml

Overview of BiocPkgTools

Shian Su, Vince Carey, Marcel Ramos, Lori Shepherd, Martin Morgan, Sean Davis

Rendered fromBiocPkgTools.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2024-01-12
Started: 2017-12-08

Readme and manuals

Help Manual

Help pageTopics
get the ORCID id from cre field of Authors@R in packageDescription result.get_cre_orcid
process employment data from ORCID.get_orcid_rec
What are the issues, pulls, commits created since a date?activitySince
Get download statistics for Bioconductor packages distributed via Anaconda.anacondaDownloadStats
Create and copy e-mail package notification template to clipboardbiocBuildEmail sentHistory
Tidy Bioconductor build report resultsbiocBuildReport
Parse the Build Report tarball for a Bioconductor releasebiocBuildReportDB
Download and parse the build status information for Bioconductor packagesbiocBuildStatusDB
Get Bioconductor download statisticsbiocDownloadStats
Explore Bioconductor packages interactivelybiocExplore
Bioconductor Maintained PackagesbiocMaintained hasBiocMaint
Get full Bioconductor software package listing, with detailsbiocPkgList
Grab build report results from BUILD_STATUS_DB for a particular package rangebiocPkgRanges
BiocPkgTools: Examine and analyze Bioconductor package metadataBiocPkgTools-package BiocPkgTools
Manage cache for BiocPkgToolsBiocPkgTools-cache pkgToolsCache setCache
Notify downstream maintainers of changes in upstream packagesbiocRevDepEmail
Work with Bioconductor package dependenciesbuildPkgDependencyDataFrame
Work with package dependencies as a graphbuildPkgDependencyIgraph
Retrieve Class relationshipsbuildClassDepData buildClassDepFromPackage buildClassDepGraph class-dependencies plotClassDep plotClassDepData plotClassDepGraph
Check the CRAN build report page and email a notificationCRANstatus
When did a package enter Bioconductor?firstInBioc
Generate a DOI for a Bioconductor packagegenerateBiocPkgDOI
Get data from Bioconductorget_bioc_data
get ORCID ids from cre fields of Authors@R in packageDescription resultsget_cre_orcids
Download a Bioconductor vignettegetBiocVignette
Generate needed information to create DOI from a package directory.getPackageInfo
Get package details from GitHubgithubDetails
Extract GitHub user and repo name from GitHub URLgithubURLParts
Return a minimal subgraph based on package name(s)inducedSubgraphByPkgs
Summary of the latest package statisticslatestPkgStats
get data.frame of employment info from orcidorcid_table
Look up a package's Bioconductor dependenciespkgBiocDeps
Obtain all the reverse dependencies for a Bioconductor packagepkgBiocRevDeps summary.biocrevdeps
Calculate dependency gain achieved by excluding combinations of packagespkgCombDependencyGain
Report package imported functionalitypkgDepImports
Report package dependency burdenpkgDepMetrics
What is a package's download rank?pkgDownloadRank
Get Bioconductor download statistics for a packagepkgDownloadStats
generate hyperlinked HTML for build reports for Bioc packagesproblemPage
Bioconductor Binary Repository Statisticsprint.repositoryStats repositoryStats
Subset graph by degreesubgraphByDegree
Obtain the location of available email templatestemplatePath