datagram/bulk_rna_seq

RNA seq analysis using Bioconductor (analysis built on limma, edgeR)

UCSF DSI RNA seq

Workshop Overview

This workshop is intended for individuals who are already comfortable with R programming and who are interested in learning to use R for standard RNA-Seq analyses. We will take you through a complete RNA-Seq workflow using R Bioconductor packages.

Learning Objectives By the end of the workshop, participants should be able to:

• Download RNA-seq files from GEO
• Annotate the samples
• Calculate expression as read counts/million (CPM) and log2(CPM)
• Filter out genes with low expression and plot
• Normalize the filtered expression data and plot
• Perform unsupervised clustering of expression data
• Perform differential expression analysis
• Create heatmaps and volcano plots
• Perform enrichment and pathway analysis

Prerequisites

You must have some R programming experience and a basic understanding of the purpose of DNA-Seq analysis to benefit from this course. Feel free to contact the instructor (see below) if you have questions about these requirements.

Software

Please have the latest versions of R and R Bioconductor installed if you plan to run the R notebooks locally. RStudio (the free version) is highly recommended as well, since we will be teaching in this environment.

We package R installations in .Rmd format - you'll need to have R, R Bioconductor, and RStudio installed to proceed.

Official UCSF DSI Course Materials

Team-reviewed, tested, and ready-to-use materials will always be hosted on our official UCSF Collaborative Learning Environment (CLE) RNA-seq webpage.

This GitHub repository is for development purposes and therefore may stray from the materials used in class. CLE will remain as it was at the time of our most recently offered workshop and will only be updated if major changes are introduced to the course.

Branch "master" should function as intended if cloned, but for verified materials please download all documents and data from CLE unless otherwise instructed.

Workshop Setup Instructions:

Please do not wait until the day of the workshop to do these installations! We cannot spend class time working through installation issues.

Installation instructions for this course are on our CLE RNA-seq webpage. If you have trouble with installations up until the day before the workshop, please email bthe instructor:

• Karla Lindquist: [email protected]

GitHub and UCSF data security protocols:

Please be aware that GitHub is not certified for use with personal health information (PHI). Do not store or share any sensitive information via GitHub, even if kept in private repositories.

For more information regarding UCSF's security guidelines, please see the UCSF IRB guidelines for electronic data security.