BiocCheck
This is the released version of BiocCheck; for the devel version, see BiocCheck.
Bioconductor-specific package checks
Bioconductor version: Release (3.23)
BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.
Author: Bioconductor Package Maintainer [aut], Lori Shepherd [aut], Daniel von Twisk [ctb], Kevin Rue [ctb], Marcel Ramos [aut, cre]
, Leonardo Collado-Torres [ctb], Federico Marini [ctb]
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("BiocCheck")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocCheck")
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("BiocCheck")| BiocCheck: Ensuring Bioconductor package guidelines | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software |
| Version | 1.48.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | BiocBaseUtils, BiocFileCache, BiocManager, biocViews, callr, cli, codetools, commonmark, graph, httr2, knitr, methods, rvest, stringdist, tools, utils, xml2 |
| System Requirements | |
| URL | https://github.com/Bioconductor/BiocCheck |
| Bug Reports | https://github.com/Bioconductor/BiocCheck/issues |
See More
| Suggests | BiocStyle, devtools, gert, jsonlite, rmarkdown, tinytest, usethis |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | AnnotationHubData, gDRstyle, methodical |
| Suggests Me | ExpoRiskR, GEOfastq, packFinder, preciseTAD, ReducedExperiment, SpatialArtifacts, SpectralTAD, HMP16SData, HMP2Data, scpdata, MainExistingDatasets, vennDiagramLab |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiocCheck_1.48.1.tar.gz |
| Windows Binary (x86_64) | BiocCheck_1.48.1.zip |
| macOS Binary (big-sur-x86_64) | BiocCheck_1.48.1.tgz |
| macOS Binary (sonoma-arm64) | BiocCheck_1.48.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiocCheck |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiocCheck |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiocCheck/ |
| Package Short Url | https://bioconductor.org/packages/BiocCheck/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |