Single Cell Proteomics EuBIC 2025 hackathon

EuBIC 2025 developers' meeting

Improving MS-based single-cell proteomics data, software and documentation

Abstract

Mass spectrometry-based single-cell proteomics (SCP) has become a credible player in the single-cell biology arena. Continuous technical improvements have pushed the boundaries of sensitivity and throughput. However, the computational efforts to support the analysis of these complex data have been lagging. The scp R/Bioconductor software is a flexible tool to handle such data. It allows to process the quantitative data, filtering and/or imputing missing values, correct batch effects, aggregate features, perform quality control and, most importantly, offers flexible and efficient support for robust and interpretable statistical modelling. In this hackathon, we propose to benefit from the broadest community input to extend the scp ecosystem to make it more accessible to a growing SCP user base.

Project Plan

In this hackathon, we propose to extend the scp ecosystem to make it more accessible to the increasing SCP user base. In particular, we would like to:

1. Identify the next set of requirements and priorities for computational SCP.
2. Improve documentation and tutorials.
3. Provide users with interactive apps and visualisation.
4. Add new data to the curated SCP data collection.
5. Prototype or develop new SCP analysis modules.

After the hackaton we plan to

• Add any deliverables to the scp package (such as new documentation/vignettes)
• Contribute new code to the respective package (scp or a GUI companion package)
• Add new datasets to scpdata
• Write a paper defining new priorities for computational SCP.

There is a range of contributions that can be expected, such as code, documentation and data, as well as discussions and interactions between computational and experimental SCP practitioners. All contributions will be formally acknowledged as package contributors (whether code or documentation) and/or authorship, depending on our productions.

Technical Details

Programming language: mostly R and shiny for the interactive features, with possible interfacing with other methods/languages. Will build on existing software: scp and QFeatures These datasets will be used/extended: scpdata

Installation instructions

• A recent version of R (>= 4.4) or one of the Bioconductor docker images.
• A set of R/Bioconductor packages that can be installed with:

install.packages("BiocManager")
BiocManager::install(c("QFeatures", "scp", "scpdata"))

Discussions

• Live, face-to-face at the hackathon
• Slack #single-cell-hackathon
• Github issues here or in the respective package repos.