In the past few years, single-cell technologies extended at an incredibly rapid pace and are now playing a central role in many biological and medical research projects. In response to the interpretation challenges they raise, hundreds of bioinformatics tools and methods have been developed to help the community analyze and visualize their single-cell data. The Single-cell omics focus group brings together SIB Members interested in these topics to share and discuss best practices and bring the field forward.

Visualizing single-cell data: a bioinformatics challenge

The recent advent of high-throughput single-cell sequencing such as scRNA-seq allowed breakthroughs in many fields (e.g., immuno-oncology) but also raised significant computational and analytical challenge. A flurry of methods covering aspects as diverse as quality control, normalization clustering, dimensionality reduction, batch-effect removal, cell-type annotation, differential analysis or trajectory inference, are available and new ones are published very week. And new assays are still emerging nowadays (multi-omics, immune receptor profiling, spatial transcriptomics), coming along with new challenges.

About the SIB focus groups

The Focus Groups aim to foster knowledge exchanges and collaborations in the community of 900 SIB Members, around specific scientific topics, from single-cell omics to epigenomics.

A SIB-wide single-cell omics Focus Group

Launched in November 2022, the group is extending the AGORA Single-Cell Omics group established by SIB Group Leader Santiago Carmona and organizes hybrid meetings every first Wednesday of the month. The group aims at discussing various topics connected to single-cell data analysis and visualization, with a focus on practical (“hands-on”) problems and new methods, benchmarks, or technologies. In 30-minutes presentations, members usually present their ongoing work, but also discuss recent articles or preprints. The presentations aim at staying informal and are followed by a discussion.

Only a couple of months after its launch, the group already has 109 members registered to the dedicated Slack channel, and meetings regularly bring together about 20 in-person attendees and 10-20 remote attendees, mostly from the SIB communities in Lausanne, Geneva, Basel, Zurich, Bern, and the local community at the AGORA Cancer Research Center in Lausanne.

Focus Group coordinating members:

Are you a SIB Member and interested in joining? Contact Santiago Carmona or Julien Roux

Zappia, L., Theis, F.J. Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape. Genome Biol 22, 301 (2021).