• Michael Love (michaelisaiahlove at gmail dot com)
• Avi Srivastava (asrivastava at nygenome dot org)

In this workshop, we will demonstrate basics of quantification of droplet-based scRNA-seq reads using alevin, producing a count matrix for import into Bioconductor using tximport/tximeta, in the end producing a SingleCellExperiment object. We will also demonstrate the ability of alevin to provide quantification uncertainty on the count matrix, and suggestions for how this information can be used in downstream analyses.

We plan the workshop to be an instructor-led live demo with time for questions and interactions with the participants.

• Basic knowledge of R syntax

Students will participate by following along a live demo, and asking questions or providing feedback throughout.

• tximport
• tximeta
• SummarizedExperiment
• SingleCellExperiment

An example for a 45-minute workshop:

• understand how scRNA-seq quantification methods work and understanding their limits
• describe how Bioconductor's classes including SingleCellExperiment facilitate reproducibility through tracking metadata on the samples/cells and the genomic ranges

• run alevin, quantifying scRNA-seq reads to make a gene count matrix
• import scRNA-seq count data including genomic ranges
• import scRNA-seq from EMBL based on experiment id
• manipulate a SingleCellExperiment
• examine distributions of scRNA-seq counts
• examine uncertainty estimates for counts