Friday, 10 June

Domain-Specific Applications and Workflows

Annotation Resources for Downstream Analyses using Bioconductor | 9:30 - 11:00 EDT

This session is devoted to annotation resources and downstream analyses of NGS data using R and Bioconductor. We will cover different annotation file formats, public resources for annotation data, and leveraging those resources for downstream analyses in R.

video

https://github.com/compbiocore/ccv_bootcamp_bioinfo/blob/2022/annot_resources.ipynb

Computational Biology Resources on Oscar | 11:00 - 11:45 EDT

We will briefly provide an overview of some of the internally developed resources that will be available on Oscar such as Refchef, SED, QCDB.

video

Introduction to Single Cell RNA-seq with Seurat | 1:00 - 2:30 EDT

We will cover the standard Seurat pre-processing pipeline for single cell RNA-seq. We will discuss working with Seurat objects, data QC and filtering, normalization, merging and integrating multiple data sets, data vizualisation, and differential expression testing.

video

https://github.com/compbiocore/scrna_r_workshop/blob/main/intro.Rmd

Advanced Topics in Single Cell RNA-seq | 2:30 - 4:00 EDT

This session continues single cell RNA-seq data analysis. We will discuss clustering QC, working with multimodal data, assigning cell type annotations, and downstream pathway analysis.

video

https://github.com/compbiocore/scrna_r_workshop/blob/main/advanced_topics.Rmd