BioC Owl: Learning about Bioconductor Objects

This is a tutorial package that familiarizes intermediate R users with aspects of Bioconductor and introduces them to the Bioconductor package ecosystem.

Learning SummarizedExperiment

The SummarizedExperiment class is one of the fundamental ways to store data in Bioconductor, whether it be protein expression, RNASeq data, or single cell data. SummarizedExperiment contains information about a studies' experimental design, and information about the genes or entities that the assay data maps to.

Learning Objectives

Learn about Bioconductor objects and how they enable complex analysis
Learn about the components of a SummarizedExperiment object and how they work together
Extract experimental information about a SummarizedExperiment object using metadata()
Learn and Utilize sample information about the experimental design of a SummarizedExperiment using colData()
Learn and utilize genomic information in rowData() to select rows based on genomic coordinates
Construct complex subsetting queries using colData() (selecting samples based on experimental design) and rowData() (selecting reads within a Genomic range using subsetByOverlap())
Utilize the Deseq2 package to run differential expression analysis using a SummarizedExperiment and a experimental design (specified by a formula)

Installing

install.packages("remotes")
remotes::install_github("laderast/biocowl")

Run the Tutorial

library(biocowl)
learn_summarized_experiment()

Acknowledgements

Based on discussions with Kate Hertweck about how to teach Bioconductor. Parts of this tutorial are derived from https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

Code of Conduct

Please note that the biocowl project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

k8hertweck / biocowl