RESOURCES

Papers and webinars that are a good starting point to familiarize yourself with the research that you will perform during the summer.   

RNA-Seq

  1. Wang et al., RNA-Seq: a revolutionary tool for transcriptomics

  2. Stark et al., RNA sequencing: the teenage years

  3. Overview of next generation sequencing platforms: https://www.youtube.com/watch?v=mI0Fo9kaWqo 

  4. Overview of Illumina sequencing platform: https://www.youtube.com/watch?v=fCd6B5HRaZ8

Single-cell RNA-Seq

  1. Haque et al., A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

  2. Introduction to Single-Cell RNA-seq

  3. Overview of single-cell sequencing

    1. https://www.youtube.com/watch?v=k9VFNLLQP8c 

    2. https://www.youtube.com/watch?v=hWWkpe4Ewgo 

R resources

  1. Swirl is an R learning package that will walk you through R programming language in a hands-on manner. Swirl will  introduce and explore various topics in the form of interactive programming assignments in R. This is a completely free and open source package. https://swirlstats.com/students.html 

  2. R for Data Science: learning R to analyze your data. “The goal of R for Data Science is to help you learn the most important tools in R that will allow you to do data science. After reading this book, you’ll have the tools to tackle a wide variety of data science challenges, using the best parts of R.” https://r4ds.had.co.nz/index.html 

  3. Run Seurat PBMC3k tutorial: Once you have familiarized yourself with R you can try running the PBMC3k tutorial. This will walk you through all the necessary steps involved in analyzing a single-cell RNA-seq data. https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

MORE RESOURCES

  1. Center for Integrated Cellular Analysis Virtual Series: https://www.multimodalintegration.org/virtualseries 

  2. Harvard University course on Computational Biology and Bioinformatics: https://youtube.com/playlist?list=PLeB-Dlq-v6tY3QLdQBA7rwb4a7fK9mLpv 

  3. Lecture 8.1. scRNA seq: https://www.youtube.com/watch?v=PFG_SKpM5OI&list=PLeB-Dlq-v6tY3QLdQBA7rwb4a7fK9mLpv&index=25

  4. Lecture 8.2. Processing and quality control scRNA seq: https://www.youtube.com/watch?v=pxLgmB0xCT0&list=PLeB-Dlq-v6tY3QLdQBA7rwb4a7fK9mLpv&index=26

  5. Lecture 8.3. scRNA-seq clustering and visualization: https://www.youtube.com/watch?v=i-e7KiETyGo&list=PLeB-Dlq-v6tY3QLdQBA7rwb4a7fK9mLpv&index=27

  6. Lecture 8.4. Differential expression in scRNA-seq: https://www.youtube.com/watch?v=kWXqKEvyw3A&list=PLeB-Dlq-v6tY3QLdQBA7rwb4a7fK9mLpv&index=28