“Bioconductor Notes, September 2025” published in The R Journal.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. The project has entered its twenty-first 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.
Bioconductor 3.21, released in April 2025, is now available. It is compatible with R 4.4 and consists of 2341 software packages, 432 experiment data packages, 928 up-to-date annotation packages, 30 workflows, and 8 books. Books are built regularly from source, ensuring full reproducibility; an example is the community-developed Orchestrating Single-Cell Analysis with Bioconductor.
Of note:
NEWS summaries for three contributed packages chosen at random from the 72 new software contributions are:
CARDspa: CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.
G4SNVHunter G-quadruplexes (G4s) are unique nucleic acid secondary structures predominantly found in guanine-rich regions and have been shown to be involved in various biological regulatory processes. G4SNVHunter is an R package designed to rapidly identify genomic sequences with G4-forming potential and accurately screen user-provided single nucleotide variants (also applicable to single nucleotide polymorphisms) that may destabilize these structures. This enables users to screen key variants for further experimental study, investigating how these variants may influence biological functions, such as gene regulation, by altering G4 formation.
jazzPanda This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordinates, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permutation testing, which is implemented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and background noise.
See the NEWS section in the release announcement for a complete account of changes throughout the ecosystem.
The December–March 2025 Outreachy program concluded successfully, with interns contributing to Bioconductor and sharing their reflections in a blog post. We also highlighted the rewarding experience of mentoring for Outreachy.
The Bioconductor community has migrated from Slack to Zulip for discussions; read more about the move here. We also reflected on our two years of Carpentries membership.
In July 2025, Bioconductor blog posts became available through R-bloggers, broadening their reach to the wider R community. One of our first posts became one of the week’s most-read, a promising sign of growing visibility. We welcome contributions to the Bioconductor blog; if you have an idea, please get in touch via Zulip or email.
Vince Carey, a long-time member of the Bioconductor Core Team, has published his reflections on the evolving complexity of the Bioconductor ecosystem in a recent journal article, “Bioconductor: Planning a third decade of comprehensive support for genomic data science”. He also shared his thoughts in a blog post, “Ask and you shall receive”.
Version 4.0.0 of ggplot2 was released on September 11, 2025. The new version introduces a significant internal change from the S3 to the S7 object system, and breakages in some Bioconductor packages that customize ggplot2’s functionality. We received early notification from ggplot2 developers through Bioconductor Zulip, and outlined the potential impact on developers and users, and provided guidance on how to adapt to this transition in a blog post in July. The ggplot2 team’s proactive communication ahead of their release helped the Bioconductor community prepare, and we appreciate their support.
We highlight several new collaborations:
The Community Advisory Board (CAB) and the Technical Advisory Board (TAB) held their annual call for new members, which closed on August 31, 2025. The selection process is currently underway, and new members will be announced later this year.
In March 2025, we published a blog post introducing Stevie Pederson as the new CAB Co-Chair. The post also highlights the role of the CAB, its working groups, and ways for community members to get involved.
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 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 Zulip 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, September 2025", The R Journal, 2025
BibTeX citation
@article{RJ-2025-2-bioconductor,
author = {Manager, Maria Doyle, Bioconductor Community and Team, Bioconductor Core Developer},
title = {Bioconductor Notes, September 2025},
journal = {The R Journal},
year = {2025},
note = {https://journal.r-project.org/news/RJ-2025-2-bioconductor},
volume = {17},
issue = {2},
issn = {2073-4859},
pages = {258-261}
}