Open Collections

Description

I will give an overview of our labâ s efforts on making the analysis of alternative splicing from RNA-seq datasets more intuitive and informative to biologists. I will introduce psichomics, a modular and extensible Bioconductor package with an intuitive Shiny-based graphical interface for alternative splicing quantification and downstream dimensionality reduction, differential splicing and gene expression and survival analyses based on The Cancer Genome Atlas, the Genotype-Tissue Expression, and the Sequence Read Archive (via recount2) projects, as well as user-provided data. These integrative analyses can incorporate clinical and molecular sample-associated features and be performed on a laptop. I will also discuss how Beta distributions can be exploited in modeling exon inclusion levels, incorporating information about the coverage-associated precision of their estimates by using the numbers of reads supporting exon inclusion and exclusion as surrogates of the distributionâ s shape parameters. Beta distributions provide a sensible framework for differential splicing analysis of small sample size datasets.