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