RNAseq

README last updated 08/10/2024

📝 Description

• Functions and analysis scripts for bulk RNAseq analysis

crick-pipeline:

• Contains functions and analysis scripts for post crick RNAseq pipeline

extract_count_mats.R

• Script for extracting count matrices from DESEq2 object output from pipeline

extractPCA.R

• Function to extract PCA and meta data dataframe from RNAseq pipeline DESeq2 object

GSEA_analysis.R

• Analysis script for GSEA

runGSEA.R

• Function for running GSEA and creating plots
• Required inputs:
  • DE_Table = the differential expression results table for the comparison of interest
  • pathways = gmt file read in by gmtfile
  • min = minimum pathway size
  • max = maximum pathway size
  • saveRes = whether results should be saved as CSV (True or False)
  • plotTop = whether top results should be plotted (True or False)
  • compName = name of differential comparison name DE table is from
  • saveDir = where outputs should be saved

custom-scripts:

• Contains any scripts that have been made for projects where some sort of custom analysis was required

qmul-hpc-scripts:

• Is an archive of old scripts previously run on QMUL HPC.

nf-core-test:

• Contains scripts for testing the nf-core pipeline