Bioconductor Classes Handbook

Package: biocclasses
Authors: Classes Working Group [aut, cre]
Compiled: 2026-03-12
Package version: 0.99.0
R version: R Under development (unstable) (2026-03-08 r89578)
BioC version: 3.23
License: Artistic-2.0

Welcome

This is the landing page of the BiocBook entitled .

This book introduces the reader to .

Docker image

A Docker image built from this repository is available here:

👉 ghcr.io/Bioconductor/classes.bioconductor.org 🐳

TipGet started now 🎉

You can get access to all the packages used in this book in < 1 minute, using this command in a terminal:

bash
docker run -it ghcr.io/Bioconductor/classes.bioconductor.org:devel R

RStudio Server

An RStudio Server instance can be initiated from the Docker image as follows:

bash
docker run \
    --volume <local_folder>:<destination_folder> \
    -e PASSWORD=OHCA \
    -p 8787:8787 \
    ghcr.io/Bioconductor/classes.bioconductor.org:devel

The initiated RStudio Server instance will be available at https://localhost:8787.

Session info

sessioninfo::session_info(
    installed.packages()[,"Package"], 
    include_base = TRUE
)
##  ─ Session info ────────────────────────────────────────────────────────────
##   setting  value
##   version  R Under development (unstable) (2026-03-08 r89578)
##   os       Ubuntu 24.04.4 LTS
##   system   x86_64, linux-gnu
##   ui       X11
##   language (EN)
##   collate  C
##   ctype    en_US.UTF-8
##   tz       Etc/UTC
##   date     2026-03-12
##   pandoc   3.9 @ /usr/bin/ (via rmarkdown)
##   quarto   1.8.25 @ /usr/local/bin/quarto
##  
##  ─ Packages ────────────────────────────────────────────────────────────────
##   package        * version date (UTC) lib source
##   askpass          1.2.1   2024-10-04 [2] CRAN (R 4.6.0)
##   base           * 4.6.0   2026-03-09 [3] local
##   base64enc        0.1-6   2026-02-02 [2] CRAN (R 4.6.0)
##   biocclasses      0.99.0  2026-03-12 [1] local
##   BiocManager      1.30.27 2025-11-14 [2] CRAN (R 4.6.0)
##   BiocStyle        2.39.0  2025-10-30 [2] Bioconductor 3.23 (R 4.6.0)
##   BiocVersion      3.23.1  2025-10-30 [2] Bioconductor 3.23 (R 4.6.0)
##   bookdown         0.46    2025-12-05 [2] CRAN (R 4.6.0)
##   boot             1.3-32  2025-08-29 [3] CRAN (R 4.6.0)
##   brew             1.0-10  2023-12-16 [2] CRAN (R 4.6.0)
##   brio             1.1.5   2024-04-24 [2] CRAN (R 4.6.0)
##   bslib            0.10.0  2026-01-26 [2] CRAN (R 4.6.0)
##   cachem           1.1.0   2024-05-16 [2] CRAN (R 4.6.0)
##   callr            3.7.6   2024-03-25 [2] CRAN (R 4.6.0)
##   class            7.3-23  2025-01-01 [3] CRAN (R 4.6.0)
##   cli              3.6.5   2025-04-23 [2] CRAN (R 4.6.0)
##   clipr            0.8.0   2022-02-22 [2] CRAN (R 4.6.0)
##   cluster          2.1.8.2 2026-02-05 [3] CRAN (R 4.6.0)
##   codetools        0.2-20  2024-03-31 [3] CRAN (R 4.6.0)
##   commonmark       2.0.0   2025-07-07 [2] CRAN (R 4.6.0)
##   compiler         4.6.0   2026-03-09 [3] local
##   cpp11            0.5.3   2026-01-20 [2] CRAN (R 4.6.0)
##   crayon           1.5.3   2024-06-20 [2] CRAN (R 4.6.0)
##   credentials      2.0.3   2025-09-12 [2] CRAN (R 4.6.0)
##   curl             7.0.0   2025-08-19 [2] CRAN (R 4.6.0)
##   datasets       * 4.6.0   2026-03-09 [3] local
##   desc             1.4.3   2023-12-10 [2] CRAN (R 4.6.0)
##   devtools         2.4.6   2025-10-03 [2] CRAN (R 4.6.0)
##   diffobj          0.3.6   2025-04-21 [2] CRAN (R 4.6.0)
##   digest           0.6.39  2025-11-19 [2] CRAN (R 4.6.0)
##   docopt           0.7.2   2025-03-25 [2] CRAN (R 4.6.0)
##   downlit          0.4.5   2025-11-14 [2] CRAN (R 4.6.0)
##   ellipsis         0.3.2   2021-04-29 [2] CRAN (R 4.6.0)
##   evaluate         1.0.5   2025-08-27 [2] CRAN (R 4.6.0)
##   fansi            1.0.7   2025-11-19 [2] CRAN (R 4.6.0)
##   fastmap          1.2.0   2024-05-15 [2] CRAN (R 4.6.0)
##   fontawesome      0.5.3   2024-11-16 [2] CRAN (R 4.6.0)
##   foreign          0.8-91  2026-01-29 [3] CRAN (R 4.6.0)
##   fs               1.6.7   2026-03-06 [2] CRAN (R 4.6.0)
##   gert             2.3.1   2026-01-11 [2] CRAN (R 4.6.0)
##   gh               1.5.0   2025-05-26 [2] CRAN (R 4.6.0)
##   gitcreds         0.1.2   2022-09-08 [2] CRAN (R 4.6.0)
##   glue             1.8.0   2024-09-30 [2] CRAN (R 4.6.0)
##   graphics       * 4.6.0   2026-03-09 [3] local
##   grDevices      * 4.6.0   2026-03-09 [3] local
##   grid             4.6.0   2026-03-09 [3] local
##   highr            0.12    2026-03-06 [2] CRAN (R 4.6.0)
##   htmltools        0.5.9   2025-12-04 [2] CRAN (R 4.6.0)
##   htmlwidgets      1.6.4   2023-12-06 [2] CRAN (R 4.6.0)
##   httpuv           1.6.16  2025-04-16 [2] CRAN (R 4.6.0)
##   httr2            1.2.2   2025-12-08 [2] CRAN (R 4.6.0)
##   ini              0.3.1   2018-05-20 [2] CRAN (R 4.6.0)
##   jquerylib        0.1.4   2021-04-26 [2] CRAN (R 4.6.0)
##   jsonlite         2.0.0   2025-03-27 [2] CRAN (R 4.6.0)
##   KernSmooth       2.23-26 2025-01-01 [3] CRAN (R 4.6.0)
##   knitr            1.51    2025-12-20 [2] CRAN (R 4.6.0)
##   later            1.4.8   2026-03-05 [2] CRAN (R 4.6.0)
##   lattice          0.22-9  2026-02-09 [3] CRAN (R 4.6.0)
##   lifecycle        1.0.5   2026-01-08 [2] CRAN (R 4.6.0)
##   littler          0.3.22  2026-02-04 [2] CRAN (R 4.6.0)
##   magrittr         2.0.4   2025-09-12 [2] CRAN (R 4.6.0)
##   MASS             7.3-65  2025-02-28 [3] CRAN (R 4.6.0)
##   Matrix           1.7-4   2025-08-28 [3] CRAN (R 4.6.0)
##   memoise          2.0.1   2021-11-26 [2] CRAN (R 4.6.0)
##   methods        * 4.6.0   2026-03-09 [3] local
##   mgcv             1.9-4   2025-11-07 [3] CRAN (R 4.6.0)
##   mime             0.13    2025-03-17 [2] CRAN (R 4.6.0)
##   miniUI           0.1.2   2025-04-17 [2] CRAN (R 4.6.0)
##   nlme             3.1-168 2025-03-31 [3] CRAN (R 4.6.0)
##   nnet             7.3-20  2025-01-01 [3] CRAN (R 4.6.0)
##   openssl          2.3.5   2026-02-26 [2] CRAN (R 4.6.0)
##   otel             0.2.0   2025-08-29 [2] CRAN (R 4.6.0)
##   parallel         4.6.0   2026-03-09 [3] local
##   pillar           1.11.1  2025-09-17 [2] CRAN (R 4.6.0)
##   pkgbuild         1.4.8   2025-05-26 [2] CRAN (R 4.6.0)
##   pkgconfig        2.0.3   2019-09-22 [2] CRAN (R 4.6.0)
##   pkgdown          2.2.0   2025-11-06 [2] CRAN (R 4.6.0)
##   pkgload          1.5.0   2026-02-03 [2] CRAN (R 4.6.0)
##   praise           1.0.0   2015-08-11 [2] CRAN (R 4.6.0)
##   preprocessCore   1.73.0  2025-10-30 [2] Bioconductor 3.23 (R 4.6.0)
##   prettyunits      1.2.0   2023-09-24 [2] CRAN (R 4.6.0)
##   processx         3.8.6   2025-02-21 [2] CRAN (R 4.6.0)
##   profvis          0.4.0   2024-09-20 [2] CRAN (R 4.6.0)
##   promises         1.5.0   2025-11-01 [2] CRAN (R 4.6.0)
##   ps               1.9.1   2025-04-12 [2] CRAN (R 4.6.0)
##   purrr            1.2.1   2026-01-09 [2] CRAN (R 4.6.0)
##   R6               2.6.1   2025-02-15 [2] CRAN (R 4.6.0)
##   ragg             1.5.1   2026-03-06 [2] CRAN (R 4.6.0)
##   rappdirs         0.3.4   2026-01-17 [2] CRAN (R 4.6.0)
##   rcmdcheck        1.4.0   2021-09-27 [2] CRAN (R 4.6.0)
##   Rcpp             1.1.1   2026-01-10 [2] CRAN (R 4.6.0)
##   remotes          2.5.0   2024-03-17 [2] CRAN (R 4.6.0)
##   rlang            1.1.7   2026-01-09 [2] CRAN (R 4.6.0)
##   rmarkdown        2.30    2025-09-28 [2] CRAN (R 4.6.0)
##   roxygen2         7.3.3   2025-09-03 [2] CRAN (R 4.6.0)
##   rpart            4.1.24  2025-01-07 [3] CRAN (R 4.6.0)
##   rprojroot        2.1.1   2025-08-26 [2] CRAN (R 4.6.0)
##   rstudioapi       0.18.0  2026-01-16 [2] CRAN (R 4.6.0)
##   rversions        3.0.0   2025-10-09 [2] CRAN (R 4.6.0)
##   sass             0.4.10  2025-04-11 [2] CRAN (R 4.6.0)
##   sessioninfo      1.2.3   2025-02-05 [2] CRAN (R 4.6.0)
##   shiny            1.13.0  2026-02-20 [2] CRAN (R 4.6.0)
##   sourcetools      0.1.7-1 2023-02-01 [2] CRAN (R 4.6.0)
##   spatial          7.3-18  2025-01-01 [3] CRAN (R 4.6.0)
##   splines          4.6.0   2026-03-09 [3] local
##   stats          * 4.6.0   2026-03-09 [3] local
##   stats4           4.6.0   2026-03-09 [3] local
##   stringi          1.8.7   2025-03-27 [2] CRAN (R 4.6.0)
##   stringr          1.6.0   2025-11-04 [2] CRAN (R 4.6.0)
##   survival         3.8-6   2026-01-16 [3] CRAN (R 4.6.0)
##   sys              3.4.3   2024-10-04 [2] CRAN (R 4.6.0)
##   systemfonts      1.3.2   2026-03-05 [2] CRAN (R 4.6.0)
##   tcltk            4.6.0   2026-03-09 [3] local
##   testthat         3.3.2   2026-01-11 [2] CRAN (R 4.6.0)
##   textshaping      1.0.5   2026-03-06 [2] CRAN (R 4.6.0)
##   tibble           3.3.1   2026-01-11 [2] CRAN (R 4.6.0)
##   tinytex          0.58    2025-11-19 [2] CRAN (R 4.6.0)
##   tools            4.6.0   2026-03-09 [3] local
##   urlchecker       1.0.1   2021-11-30 [2] CRAN (R 4.6.0)
##   usethis          3.2.1   2025-09-06 [2] CRAN (R 4.6.0)
##   utf8             1.2.6   2025-06-08 [2] CRAN (R 4.6.0)
##   utils          * 4.6.0   2026-03-09 [3] local
##   vctrs            0.7.1   2026-01-23 [2] CRAN (R 4.6.0)
##   waldo            0.6.2   2025-07-11 [2] CRAN (R 4.6.0)
##   whisker          0.4.1   2022-12-05 [2] CRAN (R 4.6.0)
##   withr            3.0.2   2024-10-28 [2] CRAN (R 4.6.0)
##   xfun             0.56    2026-01-18 [2] CRAN (R 4.6.0)
##   xml2             1.5.2   2026-01-17 [2] CRAN (R 4.6.0)
##   xopen            1.0.1   2024-04-25 [2] CRAN (R 4.6.0)
##   xtable           1.8-8   2026-02-22 [2] CRAN (R 4.6.0)
##   yaml             2.3.12  2025-12-10 [2] CRAN (R 4.6.0)
##   zip              2.3.3   2025-05-13 [2] CRAN (R 4.6.0)
##  
##   [1] /tmp/RtmpEmQxbw/Rinst8b5beb86a7
##   [2] /usr/local/lib/R/site-library
##   [3] /usr/local/lib/R/library
##   * ── Packages attached to the search path.
##  
##  ───────────────────────────────────────────────────────────────────────────
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