recount workshop: Learn to leverage 70,000 human RNA-seq samples for your projects

This workshop is for the BioC2017 meeting.

Level of difficulty



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 cover different use cases of the recount package, including downloading and normalizing data, processing and cleaning relevant phenotype data, 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.



Expected outcomes

Learn how to search projects, download data, explore the metadata, add more phenotype information, and prepare the data for a DE analysis. Then perform the DE analysis with DESeq2 and explore the results using regionReport. Participant prerequisites: basic familiarity with packages such as GenomicRanges and DESeq2. Functions from those packages used in the workshop will be briefly described.


## You will need R 3.4.x and Bioconductor 3.6 (currently Bioc-devel)

Main workshop files

Report files created in the workshop

Feedback and bug reports

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Last updated: 2017-08-01 09:52:09.