Dependencies for RNA sequencing workshop

Description:

To follow along with the practice in this course, you will use command line tools and R installed on your computer. Additionally, you will have to install the softwares and R libraries we will be using.

Full list of Dependencies:

1. Download Raw data for this course

2. Command line tools for preprocessing reads and read alignment: FASTQC STAR samtools subread

3. Download and install Interactive Genome Viewer (IGV)

4. R and its libraries for differential expression analysis: R studio

   Bioconductr libraries (check out each library for installation guide):

   • DESeq2
   • vsn
   • DEGreport
   • org.Sc.sgd.db
   • clusterProfiler

   Regular libraries (install by entering install.packages("name")):

   • tidyverse
   • ggplot2
   • dplyr
   • ggrepel
   • pheatmap

Scripts you will be using:

• Command line scripts
• R scripts

Workshop Schedule

• Introduction
• Setup using Tufts HPC
• Process Raw Reads
• Read Alignment
• Gene Quantification
• Differential Expression
• Pathway Enrichment