SIG: Current and future challenges for mass spectrometry-based omics in R/Bioconductor

[lgatto]

In this session, we would like to identify and discuss challenges and opportunities in mass spectrometry (MS)-based omics (proteomics and metabolomics) within the Bioconductor project. These topics could be user or application driven (for example development of a pipeline for SILAC quantitation), or focus more on core developments (such as, for example, using BiocFileCache for was MS data, to access local or remote data transparently). We would like, for each project identified, to provide some description, guidelines and deliverables that could be tackled collaboratively.

Some of the identified topics could form the basis of a hackathon project at the coming EuBIC developer's meeting.

Depending on the progress, we could consider drafting a opinion piece to be submitted to F1000Research to gather further input and contributions from the community.

• Topic leader: Laurent Gatto - @lgatto
• Anticipated outputs: a document describing some challenges and projects to focus on
• Chair: Laurent Gatto
• Scribe: to be determined

For people who won't be able to attend the meeting but would like to contribute, please feel free to use this issue to suggest ideas.

[jorainer]

Update on Visualize quantitative and proteomics data along genomic coordinates along with RNA-seq data: you can now use ensembldb for the mapping between genomic, transcripts and protein coordinates. Check the coordinate-mapping vignette in ensembldb - take it as a starter - if it's not doing what you expect we can always modify/improve.