We discuss general project news.
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.
In May 2024, Bioconductor 3.19 was released*. It is compatible with R 4.4 and includes 2289 software packages, 431 experiment data packages, 928 up-to-date annotation packages, 30 workflows, and 5 books. Books are built regularly from source, ensuring full reproducibility; an example is the community-developed Orchestrating Single-Cell Analysis with Bioconductor.
*Note: Bioconductor 3.20 was subsequently released in October 2024. For details on the latest release, visit the Bioconductor website.
In June 2024, the Chan Zuckerberg Initiative (CZI) announced funding for five Bioconductor projects as part of the EOSS Cycle 6. These projects focus on advancing training accessibility, developer support, GPU computing, resource tagging with ontologies, and the expansion of Tidyomics tools. For more details on each project and its collaborators, see the blog post here.
On June 12–14, 2024, Bioconductor members attended the Chan Zuckerberg Initiative (CZI) Open Science Meeting in Boston. This gathering provided an opportunity for current CZI Open Science grantees to connect and share their progress. Bioconductor was recognised as one of the top open-source software projects in the CZ Software Mentions dataset. For more details, see the blog post here.
The 20th edition of CSAMA (Computational Statistics for Biological Data Analysis) Summer School took place in Bressanone-Brixen, Italy, from June 23–28, 2024. This intensive course covered advanced analysis of molecular data using the R/Bioconductor ecosystem. Faculty included Robert Gentleman, co-founder of R and Bioconductor, and Vince Carey, current Bioconductor lead, highlighting Bioconductor’s role in open-source training.
The annual Bioconductor Conference (BioC2024) is fast approaching! This year’s event will be held in Grand Rapids, Michigan, from July 24–26, 2024. Featuring keynote talks, interactive workshops, and ample opportunities for community engagement, BioC2024 is a must-attend event for Bioconductor users and developers alike. Visit the conference website to register and learn more.
Planning is well underway for EuroBioC2024, the European Bioconductor Conference, scheduled for September 4–6, 2024, in Oxford, UK. Like BioC2024, EuroBioC2024 will include keynote presentations, hands-on workshops, and plenty of opportunities for networking with members of the Bioconductor community. For details and updates, visit the conference website.
Start using Bioconductor by installing the most recent version of R and evaluating the commands
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()Install additional packages and dependencies, e.g., SingleCellExperiment, with
BiocManager::install("SingleCellExperiment")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!
We welcome your feedback on these updates and invite you to connect with us through the Bioconductor Slack workspace or by emailing community@bioconductor.org.
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
Manager & Team, "Bioconductor Notes, June 2024", The R Journal, 2024
BibTeX citation
@article{RJ-2024-2-bioconductor,
author = {Manager, Maria Doyle, Bioconductor Community and Team, Bioconductor Core Developer},
title = {Bioconductor Notes, June 2024},
journal = {The R Journal},
year = {2024},
note = {https://journal.r-project.org/news/RJ-2024-2-bioconductor},
volume = {16},
issue = {2},
issn = {2073-4859},
pages = {1}
}