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nih-cfde / 2022-may-hackathon

https://nih-cfde.github.io/2022-may-hackathon/
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Introduction to R for RNA Sequencing Analysis with GTEx Data #8

Open raynamharris opened 2 years ago

raynamharris commented 2 years ago

RNA-Sequencing (RNA-Seq) is a popular method for determining the presence and quantity of RNA in biological samples. In this 3 hour workshop, we will use R to explore publicly-available RNA-Seq data from the Gene Expression Tissue Project (GTEx). Attendees will be introduced to the R syntax, variables, functions, packages, and data structures common to RNA-Seq projects. We will use RStudio to import, tidy, transform, and visualize RNA-Seq count data. Attendees will learn tips and tricks for making the processes of data wrangling and data harmonization more manageable. This workshop will not cover cloud-based workflows for processing RNA-seq reads or statistics and modeling because these topics are covered in our RNA-Seq Concepts and RNA-Seq in the Cloud workshops. Rather, this workshop will focus on general R concepts applied to RNA-Seq data. Familiarity with R is not required but would be useful.

raynamharris commented 2 years ago

Notes: https://hackmd.io/7mrklXMGTBa2GAjzhFtZ1A

jessicalumian commented 2 years ago

Instructional materials: https://hackmd.io/MsWY1O9GQXGVDl2OmV2jxg?view

One of Rayna's favorite papers on gene name problems: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7

R for Data Science (great book!): https://r4ds.had.co.nz/

GitHub repo of R code: https://github.com/nih-cfde/training-rstudio-binder/

Hex Color Picker: https://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3