Skip to contents

Bioconductor Repositories

Kevin Rue-Albrecht

University of Oxford

16 March 2026

Repositories.Rmd

Libraries

Attach packages used in this vignettes.

library("BiocPkgTools")
#> Loading required package: htmlwidgets
library("BiocPkgToolsPlus")
#> Loading required package: biocViews
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

First step

Fetch the combined listing of packages from all Bioconductor repositories.

bioc_pkg_list <- get_all_biocpkglist(verbose = FALSE)
bioc_pkg_list
#> # A tibble: 3,753 × 49
#>    Package     Version Depends   Suggests  License MD5sum NeedsCompilation Title
#>    <chr>       <chr>   <list>    <list>    <chr>   <chr>  <chr>            <chr>
#>  1 a4          1.58.0  <chr [5]> <chr [7]> GPL-3   56d24… no               "Aut…
#>  2 a4Base      1.58.0  <chr [2]> <chr [4]> GPL-3   5efa1… no               "Aut…
#>  3 a4Classif   1.58.0  <chr [2]> <chr [4]> GPL-3   20d28… no               "Aut…
#>  4 a4Core      1.58.0  <chr [1]> <chr [2]> GPL-3   bd94b… no               "Aut…
#>  5 a4Preproc   1.58.0  <chr [1]> <chr [4]> GPL-3   2c56d… no               "Aut…
#>  6 a4Reporting 1.58.0  <chr [1]> <chr [2]> GPL-3   9d31f… no               "Aut…
#>  7 ABarray     1.78.0  <chr [1]> <chr [2]> GPL     6ad7c… no               "Mic…
#>  8 abseqR      1.28.0  <chr [1]> <chr [1]> GPL-3 … 9ec04… no               "Rep…
#>  9 ABSSeq      1.64.0  <chr [2]> <chr [1]> GPL (>… b12fd… no               "ABS…
#> 10 acde        1.40.0  <chr [2]> <chr [2]> GPL-3   c04fa… no               "Art…
#> # ℹ 3,743 more rows
#> # ℹ 41 more variables: Description <chr>, biocViews <list>, Author <list>,
#> #   Maintainer <list>, git_url <chr>, git_branch <chr>, git_last_commit <chr>,
#> #   git_last_commit_date <chr>, `Date/Publication` <chr>, source.ver <chr>,
#> #   win.binary.ver <chr>, `mac.binary.big-sur-x86_64.ver` <chr>,
#> #   `mac.binary.big-sur-arm64.ver` <chr>, vignettes <list>,
#> #   vignetteTitles <list>, hasREADME <chr>, hasNEWS <chr>, hasINSTALL <chr>, …

Reminder of the Bioconductor repositories fetched from (along with the number of packages found in each of them):

bioc_pkg_list |> 
  summarise(Packages = n(), .by = Repository)
#> # A tibble: 4 × 2
#>   Repository    Packages
#>   <fct>            <int>
#> 1 BioCsoft          2361
#> 2 BioCexp            435
#> 3 BioCworkflows       29
#> 4 BioCann            928

Software 

get_packages_by_view("BatchEffect", pkg_list = bioc_pkg_list) |> 
  filter(Repository == "BioCsoft")
#> # A tibble: 74 × 2
#>    Package    Repository
#>    <chr>      <fct>     
#>  1 affylmGUI  BioCsoft  
#>  2 AMARETTO   BioCsoft  
#>  3 anglemania BioCsoft  
#>  4 anota2seq  BioCsoft  
#>  5 bacon      BioCsoft  
#>  6 batchCorr  BioCsoft  
#>  7 batchelor  BioCsoft  
#>  8 BatchQC    BioCsoft  
#>  9 BatchSVG   BioCsoft  
#> 10 BEclear    BioCsoft  
#> # ℹ 64 more rows

Annotations 

get_packages_by_view("GenomicSequence", pkg_list = bioc_pkg_list) |> 
  filter(Repository == "BioCann")
#> # A tibble: 4 × 2
#>   Package             Repository
#>   <chr>               <fct>     
#> 1 CTCF                BioCann   
#> 2 excluderanges       BioCann   
#> 3 LymphoSeqDB         BioCann   
#> 4 TENET.AnnotationHub BioCann

Workflows 

get_packages_by_view("SingleCellWorkflow", pkg_list = bioc_pkg_list) |> 
  filter(Repository == "BioCworkflows")
#> # A tibble: 2 × 2
#>   Package          Repository   
#>   <chr>            <fct>        
#> 1 cytofWorkflow    BioCworkflows
#> 2 simpleSingleCell BioCworkflows

Experiments 

get_packages_by_view("MassSpectrometryData", pkg_list = bioc_pkg_list) |> 
  filter(Repository == "BioCexp")
#> # A tibble: 26 × 2
#>    Package           Repository
#>    <chr>             <fct>     
#>  1 adductData        BioCexp   
#>  2 AWAggregatorData  BioCexp   
#>  3 BioPlex           BioCexp   
#>  4 CardinalWorkflows BioCexp   
#>  5 CluMSIDdata       BioCexp   
#>  6 DAPARdata         BioCexp   
#>  7 faahKO            BioCexp   
#>  8 gcspikelite       BioCexp   
#>  9 iModMixData       BioCexp   
#> 10 metaMSdata        BioCexp   
#> # ℹ 16 more rows

Reproducibility

The BiocPkgToolsPlus package (kevinrue, 2026) was made possible thanks to:

  • R (R Core Team, 2025)
  • BiocStyle (Oleś, 2025)
  • knitr (Xie, 2025)
  • RefManageR (McLean, 2017)
  • rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2025)
  • sessioninfo (Wickham, Chang, Flight, Müller, and Hester, 2025)
  • testthat (Wickham, 2011)

This package was developed using biocthis.

Code for creating the vignette

## Create the vignette
library("rmarkdown")
system.time(render("BiocPkgToolsPlus.Rmd", "BiocStyle::html_document"))

## Extract the R code
library("knitr")
knit("BiocPkgToolsPlus.Rmd", tangle = TRUE)

Date the vignette was generated.

#> [1] "2026-03-16 08:57:10 UTC"

Wallclock time spent generating the vignette.

#> Time difference of 6.463 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.5.2 (2025-10-31)
#>  os       Ubuntu 24.04.3 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       UTC
#>  date     2026-03-16
#>  pandoc   3.8.2.1 @ /usr/bin/ (via rmarkdown)
#>  quarto   1.7.32 @ /usr/local/bin/quarto
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package          * version   date (UTC) lib source
#>  backports          1.5.0     2024-05-23 [1] RSPM (R 4.5.0)
#>  bibtex             0.5.2     2026-02-03 [1] RSPM (R 4.5.0)
#>  Biobase            2.70.0    2025-10-29 [1] Bioconductor 3.22 (R 4.5.2)
#>  BiocFileCache      3.0.0     2025-10-29 [1] Bioconductor 3.22 (R 4.5.2)
#>  BiocGenerics       0.56.0    2025-10-29 [1] Bioconductor 3.22 (R 4.5.2)
#>  BiocManager        1.30.27   2025-11-14 [2] CRAN (R 4.5.2)
#>  BiocPkgTools     * 1.28.3    2026-02-05 [1] Bioconductor 3.22 (R 4.5.2)
#>  BiocPkgToolsPlus * 0.99.0    2026-03-16 [1] Bioconductor
#>  BiocStyle        * 2.38.0    2025-10-29 [1] Bioconductor 3.22 (R 4.5.2)
#>  biocViews        * 1.78.0    2025-10-29 [1] Bioconductor 3.22 (R 4.5.2)
#>  bit                4.6.0     2025-03-06 [1] RSPM (R 4.5.0)
#>  bit64              4.6.0-1   2025-01-16 [1] RSPM (R 4.5.0)
#>  bitops             1.0-9     2024-10-03 [1] RSPM (R 4.5.0)
#>  blob               1.3.0     2026-01-14 [1] RSPM (R 4.5.0)
#>  bookdown           0.46      2025-12-05 [1] RSPM (R 4.5.0)
#>  bslib              0.10.0    2026-01-26 [2] RSPM (R 4.5.0)
#>  cachem             1.1.0     2024-05-16 [2] RSPM (R 4.5.0)
#>  cli                3.6.5     2025-04-23 [2] RSPM (R 4.5.0)
#>  curl               7.0.0     2025-08-19 [2] RSPM (R 4.5.0)
#>  DBI                1.3.0     2026-02-25 [1] RSPM (R 4.5.0)
#>  dbplyr             2.5.2     2026-02-13 [1] RSPM (R 4.5.0)
#>  desc               1.4.3     2023-12-10 [2] RSPM (R 4.5.0)
#>  digest             0.6.39    2025-11-19 [2] RSPM (R 4.5.0)
#>  dplyr            * 1.2.0     2026-02-03 [1] RSPM (R 4.5.0)
#>  DT                 0.34.0    2025-09-02 [1] RSPM (R 4.5.0)
#>  evaluate           1.0.5     2025-08-27 [2] RSPM (R 4.5.0)
#>  fastmap            1.2.0     2024-05-15 [2] RSPM (R 4.5.0)
#>  filelock           1.0.3     2023-12-11 [1] RSPM (R 4.5.0)
#>  fs                 1.6.7     2026-03-06 [2] RSPM (R 4.5.0)
#>  generics           0.1.4     2025-05-09 [1] RSPM (R 4.5.0)
#>  gh                 1.5.0     2025-05-26 [2] RSPM (R 4.5.0)
#>  glue               1.8.0     2024-09-30 [2] RSPM (R 4.5.0)
#>  graph              1.88.1    2025-12-08 [1] Bioconductor 3.22 (R 4.5.2)
#>  hms                1.1.4     2025-10-17 [1] RSPM (R 4.5.0)
#>  htmltools          0.5.9     2025-12-04 [2] RSPM (R 4.5.0)
#>  htmlwidgets      * 1.6.4     2023-12-06 [2] RSPM (R 4.5.0)
#>  httr               1.4.8     2026-02-13 [1] RSPM (R 4.5.0)
#>  httr2              1.2.2     2025-12-08 [2] RSPM (R 4.5.0)
#>  igraph             2.2.2     2026-02-12 [1] RSPM (R 4.5.0)
#>  jquerylib          0.1.4     2021-04-26 [2] RSPM (R 4.5.0)
#>  jsonlite           2.0.0     2025-03-27 [2] RSPM (R 4.5.0)
#>  knitr              1.51      2025-12-20 [2] RSPM (R 4.5.0)
#>  lifecycle          1.0.5     2026-01-08 [2] RSPM (R 4.5.0)
#>  lubridate          1.9.5     2026-02-04 [1] RSPM (R 4.5.0)
#>  magrittr           2.0.4     2025-09-12 [2] RSPM (R 4.5.0)
#>  memoise            2.0.1     2021-11-26 [2] RSPM (R 4.5.0)
#>  otel               0.2.0     2025-08-29 [2] RSPM (R 4.5.0)
#>  pillar             1.11.1    2025-09-17 [2] RSPM (R 4.5.0)
#>  pkgconfig          2.0.3     2019-09-22 [2] RSPM (R 4.5.0)
#>  pkgdown            2.2.0     2025-11-06 [2] RSPM (R 4.5.0)
#>  plyr               1.8.9     2023-10-02 [1] RSPM (R 4.5.0)
#>  purrr              1.2.1     2026-01-09 [2] RSPM (R 4.5.0)
#>  R6                 2.6.1     2025-02-15 [2] RSPM (R 4.5.0)
#>  ragg               1.5.1     2026-03-06 [2] RSPM (R 4.5.0)
#>  rappdirs           0.3.4     2026-01-17 [2] RSPM (R 4.5.0)
#>  RBGL               1.86.0    2025-10-29 [1] Bioconductor 3.22 (R 4.5.2)
#>  Rcpp               1.1.1     2026-01-10 [2] RSPM (R 4.5.0)
#>  RCurl              1.98-1.17 2025-03-22 [1] RSPM (R 4.5.0)
#>  readr              2.2.0     2026-02-19 [1] RSPM (R 4.5.0)
#>  RefManageR       * 1.4.0     2022-09-30 [1] RSPM (R 4.5.0)
#>  rlang              1.1.7     2026-01-09 [2] RSPM (R 4.5.0)
#>  rmarkdown          2.30      2025-09-28 [2] RSPM (R 4.5.0)
#>  RSQLite            2.4.6     2026-02-06 [1] RSPM (R 4.5.0)
#>  RUnit              0.4.33.1  2025-06-17 [1] RSPM (R 4.5.0)
#>  rvest              1.0.5     2025-08-29 [1] RSPM (R 4.5.0)
#>  sass               0.4.10    2025-04-11 [2] RSPM (R 4.5.0)
#>  sessioninfo      * 1.2.3     2025-02-05 [2] RSPM (R 4.5.0)
#>  stringi            1.8.7     2025-03-27 [2] RSPM (R 4.5.0)
#>  stringr            1.6.0     2025-11-04 [2] RSPM (R 4.5.0)
#>  systemfonts        1.3.2     2026-03-05 [2] RSPM (R 4.5.0)
#>  textshaping        1.0.5     2026-03-06 [2] RSPM (R 4.5.0)
#>  tibble             3.3.1     2026-01-11 [2] RSPM (R 4.5.0)
#>  tidyr              1.3.2     2025-12-19 [1] RSPM (R 4.5.0)
#>  tidyselect         1.2.1     2024-03-11 [1] RSPM (R 4.5.0)
#>  timechange         0.4.0     2026-01-29 [1] RSPM (R 4.5.0)
#>  tzdb               0.5.0     2025-03-15 [1] RSPM (R 4.5.0)
#>  utf8               1.2.6     2025-06-08 [2] RSPM (R 4.5.0)
#>  vctrs              0.7.1     2026-01-23 [2] RSPM (R 4.5.0)
#>  withr              3.0.2     2024-10-28 [2] RSPM (R 4.5.0)
#>  xfun               0.56      2026-01-18 [2] RSPM (R 4.5.0)
#>  XML                3.99-0.22 2026-02-10 [1] RSPM (R 4.5.0)
#>  xml2               1.5.2     2026-01-17 [2] RSPM (R 4.5.0)
#>  yaml               2.3.12    2025-12-10 [2] RSPM (R 4.5.0)
#> 
#>  [1] /__w/_temp/Library
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/local/lib/R/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Bibliography

This vignette was generated using BiocStyle (Oleś, 2025) with knitr (Xie, 2025) and rmarkdown (Allaire, Xie, Dervieux et al., 2025) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.30. 2025. URL: https://github.com/rstudio/rmarkdown.

[2] kevinrue. Demonstration of a Bioconductor Package. https://github.com/kevinrue/BiocPkgToolsPlus/BiocPkgToolsPlus - R package version 0.99.0. 2026. DOI: 10.18129/B9.bioc.BiocPkgToolsPlus. URL: http://www.bioconductor.org/packages/BiocPkgToolsPlus.

[3] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.

[4] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.38.0. 2025. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.

[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2025. URL: https://www.R-project.org/.

[6] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/articles/RJ-2011-002/.

[7] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.3. 2025. URL: https://github.com/r-lib/sessioninfo#readme.

[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.51. 2025. URL: https://yihui.org/knitr/.