MEDS5420 - Lectures 24, 25, & 26 - Differential expression
April 17, 19, & 24 2023
Contents
1
Review and RNA-seq differential gene expression analysis workflow:
2
Counting with HTseq
3
a review of running
R
on Xanadu
4
The preamble: load libraries and functions
5
Converting the counts table text files into an
R
dataframe
6
Repetitive process? Make a function in
R
!
7
General use of the
HTSeq
to
R
data frame function
8
Prepping data for
DESeq2
8.1
Note on factor levels (this is verbatim from the DESeq2 Guide)
8.2
Running
DESeq2
8.3
Visualizing experiment clustering
8.4
Identifying and plotting activated and repressed genes
8.5
Converting gene IDs to gene names
9
Gene Set Enrichment Analysis
9.1
Order a gene list
9.2
Get the curated gene list
9.3
FGSEA
9.4
Panther
9.5
BART
1
Review and RNA-seq differential gene expression analysis workflow: