Apps and frameworks

Short talk: unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level

unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level Emanuela Iovino,Tommaso Pippucci,Marco Seri University of Bologna Abstract Motivation Next-generation sequencing is increasingly adopted in the clinical practice largely thanks to concurrent advancements in bioinformatic tools for variant detection and annotation. However, the need to assess sequencing quality at the base-pair level still poses challenges for diagnostic accuracy. One of the most popular quality parameters is the percentage of targeted bases characterized by low depth of coverage (DoC).

Short talk: Omics Playground: A user-friendly and interactive self-service bioinformatics platform for the in-depth analysis, visualisation and interpretation of transcriptomics and proteomics data

Omics Playground: A user-friendly and interactive self-service bioinformatics platform for the in-depth analysis, visualisation and interpretation of transcriptomics and proteomics data Murodzhon Akhmedov,Axel Martinelli,Ivo Murodzhon BigOmics Analytics Abstract Omics Playground is a user-friendly and interactive self-service bioinformatics platform for the in-depth analysis, visualisation and interpretation of transcriptomics and proteomics data. It is implemented in R using the Shiny web application framework and provides access to a large number of bioconductor modules that include data quality checks, clustering analysis, standard pairwise comparisons, gene set enrichment analysis and biomarker discovery among others.

Short talk: MISTy: Multiview Intercellular SpaTial modeling framework

MISTy: Multiview Intercellular SpaTial modeling framework Jovan Tanevski,Attila Gabor,Ricardo Omar Ramirez Flores,Denis Schapiro,Julio Saez-Rodriguez Heidelberg University & Heidelberg University Hospital Abstract The proliferation of different technologies for measuring rich spatial omics requires flexible and scalable tools for their analysis. We present MISTy a package for knowledge discovery and analysis of highly multiplexed spatial omics data by explainable multi-view machine learning. It can be readily applied to samples containing up to millions of spatial units and thousands of markers.

Short talk: Bioconductor framework for consistent annotation of hyperpolymorphic HLA genes in human populations

Bioconductor framework for consistent annotation of hyperpolymorphic HLA genes in human populations Katharina Imkeller,Wolfgang Huber European Molecular Biology Laboratory Heidelberg Abstract MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. This process, also known as MHC-dependent antigen presentation, is essential for the coordination of adaptive immune responses. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus on chromosome 6.