Anthony Federico (anfed@bu.edu)
Section of Computational Biomedicine
Boston University
Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in generating workflows that enable efficient analysis and are highly reproducible, particularly when dealing with many signatures across multiple experiments. In this workshop, we will demonstrate how hypeR - an R package for geneset enrichment workflows - addresses these issues and more.
We recommend the latest version of R (>= 4.0.0) but hypeR currently requires R (>= 3.6.0) to be installed directly from Github or Bioconductor. To install with R (>= 3.5.0) see below. Use with R (< 3.5.0) is not recommended.
Install the development version of the package from Github. {r, eval=FALSE} devtools::install_github("montilab/hypeR")
Or install the development version of the package from Bioconductor. {r, eval=FALSE} BiocManager::install("montilab/hypeR", version="devel")
Students will participate by following along a markdown document, trying variations of provided code, and asking questions throughout the workshop.
| Activity | Time |
|---|---|
| Geneset Enrichment 101 | ~10 min |
| Introduction to hypeR | ~5 min |
| Downloading Genesets | ~5 min |
| hypeR Methods | ~5 min |
| Relational Genesets | ~5 min |
| Handling Many Signatures | ~5 min |
| Workflow Reproducibility | ~5 min |
| Rmarkdown and Shiny | ~5 min |
| Questions | Interruptions Welcome |
Learning Goals
Learning Objectives