Bioconductor Notes

“Bioconductor Notes” published in The R Journal.

Maria Doyle (University of Limerick,Bioconductor Community Manager) , Bioconductor Core Developer Team (Dana-Farber Cancer Institute, Roswell Park Comprehensive Cancer Center, City University of New York, Fred Hutchinson Cancer Research Center, Mass General Brigham)


Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. The project has entered its twentieth year, with funding for core development and infrastructure maintenance secured through 2025 (NIH NHGRI 2U24HG004059). Additional support is provided by NIH NCI, Chan-Zuckerberg Initiative, National Science Foundation, Microsoft, and Amazon. In this news report, we give some updates on core team and project activities.


The current Bioconductor release is 3.16. It is compatible with R 4.2 and consists of 2183 software packages, 416 experiment data packages, 909 up-to-date annotation packages, 28 workflows, and 3 books. are built regularly from source and therefore fully reproducible; an example is the community-developed Orchestrating Single-Cell Analysis with Bioconductor.

Bioconductor in Python!

We’re excited to introduce BiocPy, a project aimed at enabling Bioconductor workflows in Python. Analysts today use a variety of languages in their workflows, including R/Bioconductor for statistical analysis and Python for imaging or machine learning tasks. BiocPy aims to facilitate interoperability between R and Python by providing standardized data structures based on existing Bioconductor data structures. These include genomic ranges for interval based operations, summarized experiments and other derivatives for analyzing genomic experiments. To learn more, visit the BiocPy GitHub organization.

Core team updates

Default Branch Renaming

The default branch (that corresponds to Bioconductor devel version) will be renamed to devel on for all packages to move forward with diversity and inclusiveness. The core has been doing extensive testing and is ready to move forward within the next 2-3 weeks.

Maintainers will temporarily still be able to push to either devel or master to allow time for adaptation, with the goal of eventually making it an error in maybe 2-3 release cycles (1-1.5 years) We will be making announcements on bioc-devel mailing list, Twitter, Mastodon, Slack, etc with an upcoming/heads up and an announcement when it is live.

Partnering with Outreachy

Bioconductor participated as a mentoring community in Outreachy’s December 2022 - March 2023 internship round. Outreachy provides open source and open science internships to individuals impacted by systemic bias and underrepresentation in tech. Bioconductor received funding for two interns through Outreachy’s general fund for two projects. Kirabo Atuhurira, a software engineering student from Kampala, Uganda, was chosen to work on the BSgenomeForge, which attempts to simplify making Bsgenome data packages. Beryl Kanali, a masters student from Nairobi, Kenya, was chosen to work on Sweave2Rmd, which attempts to modernize Sweave vignettes by converting them into R Markdown. You can read more about their experience at Our experience as Outreachy interns with Bioconductor.

Bioconductor will also participate in Outreachy’s May 2023 - August 2023 internship round to offer internships with Bioconductor community projects.


The BioC2023 and EuroBioC2023 conferences have both been announced, and abstract submissions are open. BioC Asia 2023 will be announced later this year.

BioC2023 will be held in Boston, USA from Aug 2-4. Abstracts can be submitted until March 19.

EuroBioC2023 will be held in Ghent, Belgium from Sep 20-22. Abstracts can be submitted until April 14.


The Bioconductor blog is used for articles of interest by and for the community. Recent articles include:

Boards updates

Community Advisory Board

Committees and Working groups updates

If you are interested in becoming involved with one of these groups please contact the group leader(s).


Using Bioconductor

Start using Bioconductor by installing the most recent version of R and evaluating the commands

  if (!requireNamespace("BiocManager", quietly = TRUE))

Install additional packages and dependencies, e.g., SingleCellExperiment, with


Docker images provides a very effective on-ramp for power users to rapidly obtain access to standardized and scalable computing environments. Key resources include:

Upcoming and recently completed events are browsable at our events page.

The Technical and and Community Advisory Boards provide guidance to ensure that the project addresses leading-edge biological problems with advanced technical approaches, and adopts practices (such as a project-wide Code of Conduct that encourages all to participate. We look forward to welcoming you!



Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".


For attribution, please cite this work as

Doyle & Team, "The R Journal: Bioconductor Notes", The R Journal, 2022

BibTeX citation

  author = {Doyle, Maria and Team, Bioconductor Core Developer},
  title = {The R Journal: Bioconductor Notes},
  journal = {The R Journal},
  year = {2022},
  note = {},
  volume = {14},
  issue = {4},
  issn = {2073-4859},
  pages = {352-355}