Leonardo Collado-Torres
The recount2 project re-processed RNA sequencing (RNA-seq) data on over 70,000 human RNA-seq samples spanning a variety of tissues, cell types and disease conditions. Researchers can easily access these data via the recount Bioconductor package, and can quickly import gene, exon, exon-exon junction and base-pair coverage data for uniformly processed data from the SRA, GTEx and TCGA projects in R for analysis. This workshop will include an overview of the recount2 project as well as methods and tools that have been to improve it since 2017. The overview will be followed by a hands-on session where you will dive into recount and related packages along the lines of the recount workflow.
In more detail, this workshop will cover different use cases of the recount package, including downloading and normalizing data, processing and cleaning relevant phenotype data (including recount-brain), performing differential expression (DE) analyses, and creating reports for exploring the results using other Bioconductor packages. The workshop will also cover how to use the base-pair coverage data for annotation-agnostic DE analyses and for visualizing coverage data for features of interest. After taking this workshop, attendees will be ready to enhance their analyses by leveraging RNA-seq data from 70,000 human samples.
recount2 website, recount package, paper, recount workflow.
- Basic knowledge of R syntax
- Basic knowledge of RNA-seq or gene expression data
- Familiarity with the RangedSummarizedExperiment class
- Familiarity with SummarizedExperiment vignette
If you are curious, we taught a similar workshop at BioC2017 that will be updated for this BioC2019. That original workshop lead to the recount workflow which we also plan to update this year.
Students are expected to ask questions during the recount2 overview presentation and to bring their own laptop so they can follow the hands-on portion of the workshop.
SummarizedExperiment, recount, GenomicRanges, DESeq2, derfinder, regionReport are among the packages that will be explicitly covered.
| Activity | Time |
|---|---|
| recount2 project and updates overview | 30m |
| break 1 / package setup and troubleshooting | 5 min |
| accessing gene count data with recount | 15m |
| using recount-brain | 15m |
| break 2 | 5 min |
| in depth example analysis | 30m |
| closing remarks | 5m |
Total: 1h 45 min.
- Understand the publicly data available via the recount2 project beyond gene counts
- Identify how recount2 data could be useful for your RNA-seq projects and how you can use it
- Describe the annotation-agnostic methods powered by recount2 that complement other RNA-seq analysis pipelines
- Re-analyze public RNA-seq data using the recount Bioconductor package
- Recognize how to access the different types of data hosted by recount2
- Locate resources that enhance recount2 such as recount-brain and review how to use them
- Produce a HTML report of a differential expression analysis