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Abstract:

In a keynote at GBCC 2025, Dr. Charlotte Soneson discusses how the Bioconductor project—beyond its software packages—has fundamentally shaped her research. She highlights the crucial role of the Bioconductor community, conferences, and shared infrastructure through two distinct examples.

The first example is iSEE, an interactive visualization tool for single-cell data, which originated from a collaboration at a Bioconductor conference. Its success and broad applicability are directly attributed to its foundation on the standardized SummarizedExperiment data class, a core Bioconductor structure.

The second example is footprinter, a package for analyzing high-resolution, single-molecule footprinting data from nanopore sequencing. The project faced a significant challenge in representing sparse read-level data, which was resolved through a direct collaboration with the Bioconductor core team. This led to the creation of a novel NA_matrix class, enabling efficient and unambiguous data storage and analysis. Dr. Soneson demonstrates how this allows for highly sensitive detection of biological features like nucleosome phasing, surpassing traditional assays. Ultimately, the talk underscores that Bioconductor's true power lies in its combination of community collaboration and robust, forward-looking technical infrastructure.

The Broader Impact of Bioconductor: From Community to Code

• 00:01:06 Main Thesis: The talk explores how Bioconductor's impact extends beyond its packages to its community, conferences, focus on standard classes, and core team, using two software packages as examples.
• 00:01:46 Example 1: The iSEE Package: The development of iSEE, an interactive visualization application, began at the 2017 European Bioconductor conference during a special interest group meeting, highlighting the importance of the community and in-person events for fostering collaboration.
• 00:03:21 The Power of Standardization: iSEE was built to use the SummarizedExperiment class as its primary input. This standardized data container, widely used across Bioconductor, allows iSEE to be a general-purpose tool for many types of matrix-like biological data, not just single-cell.
• 00:07:14 Linked Selections for Data Exploration: A key feature of iSEE is the ability to link panels. Users can select data points in one plot (e.g., cells in a t-SNE) and see the corresponding information immediately updated in other panels (e.g., a table of marker genes and a corresponding heatmap).
• 00:08:49 Ensuring Reproducibility: iSEE allows users to extract the underlying R code required to generate any plot seen in the interface, ensuring that interactive explorations can be fully reproduced and documented.
• 00:09:50 A Growing Ecosystem: The iSEE package has spawned a larger "iSEEverse" of extension packages and is now used to create interactive supplementary materials for scientific papers, complete with guided tours for readers.
• 00:15:43 Example 2: The footprinter Package: The second example is a new package for analyzing complex, single-molecule footprinting data generated by nanopore sequencing, which provides base-level resolution of DNA accessibility.
• 00:22:32 The Challenge of Sparse, High-Resolution Data: This data is massive and sparse at the single-read level. Standard sparse matrices were unsuitable because they represent unobserved positions as zero, making it impossible to distinguish them from positions that were observed to be unmodified (also zero).
• 00:29:07 A Core Team Collaboration: The problem was solved by collaborating with Hervé Pagès of the Bioconductor core team, who developed a new sparse matrix class (NA_matrix) that uses NA for unobserved values. This was a critical innovation that made the project feasible.
• 00:40:55 High-Sensitivity Biological Insights: Using this new data structure, footprinter can perform highly sensitive analyses. Dr. Soneson shows that it can detect nucleosome phasing changes with greater sensitivity than traditional ChIP-seq, offering a more powerful way to infer transcription factor binding.
• 00:47:42 Conclusion: Bioconductor's Essential Role: The development of both iSEE and footprinter was critically dependent on the Bioconductor ecosystem—the former on its community and standardized classes, and the latter on direct, problem-solving collaboration with its core development team.