SIG: Extending gene set and signature representations #25
Introduction of yourself:
Lluís Revilla Sancho, a PhD student interested in gene sets and how to store and analyse cell signatures, pathways and sets related to diseases, process and state of the cells as a way to learn more insight in the biology of the cells. Developer of BioCor, and contributor to other packages included in Bioconductor such as GOSemSim, fgsea.
Kevin Rue-Albrecht, a postdoctoral researcher in computational biology at the University of Oxford. My main interests are in immunology and (single-cell) transcriptomics. My background includes a MSc in Bioengineering, Bioinformatics and Modelling for Biology, and a PhD in Computational Infection Biology. Contributions to Bioconductor include GOexpress, TVTB, and iSEE.
Kayla Morrell is a developer at Bioconductor.
Should it be held during Developer Day?
Description of the topic:
The recent development of high throughput genomics technologies facilitated the generation several data types: single cell expression, methylation, chromatin disponibility, microorganism presence and transcriptome, proteomics, metabolomics, T cell receptors, B-cell receptors, etc. A current research interest uses several of these features to accurately describe phenotypes. For instance, single-cell expression is usually relevant to define new cell lines using a group of genes being expressed. But with other types of data new classes should be created in the GSEABase package. However, this new classes would not overcome the slowness of the existing structure nor improve the ease of use to new users.
Over the lasts months a coordinated effort among members of the Bioconductor community has explored possibilities for novel gene set containers. We have discussed how a new class could solve this problems, (a public record can be found here). We developed new containers with the GSEABase functionality, while simplifying internally the structure in three tables (one for elements, one for sets and one for the relationships between them), allowing non-quoted evaluation. Three packages were developed to explore different implementations:
This special interest group session will provide a summary of what was done in the past months by each developer, hear their feedback and plan accordingly taking into account the project aims:
In the birds-of-a-feather session we will discuss the proposed software aimed at the analysis of sets. Explore the needs and desires of other developers currently using GSEABase classes and explore what the users and developers might need.
Secondary outputs could include code, notebooks, gists, documentation, and opening issues on the existing repositories.