stunning-fiesta

TCGA Assemble RJB

Using adopted scripts from Jack's 'TCGA_Assemble' repo.

Functions Script

In the Functions folder is a script with all key functions written by Jack for processing.

LUAD_Read_V1.0

The 'luadread_tcga_pancancer.R' has all the pre-processing scripts for TCGA PanCancer Atlas for each of the following data:

1. Clinical
2. CNA (this data file is too big to be opened using Excel)
3. RNA-Seq - both median RPKM values and z-scores collated into one file (also too big to be opened in Excel)
4. Mutations
5. Fusions

Analyse_Data_V1.0/Mutations

The 'luad_pancancer_mut_analysis.R' script has the following analyses which were done in April 2019:

1. Rough types and number of total mutations/patient
2. Detailed type of mutation
3. Protein change positions
4. Amino acid changes

The 'luad_pancancer_mut_subsetting.R' script was used in April 2019: Used to subset predominatly KRAS single, STK11 single and KRAS/STK11 double mutation patients.

Gene_Sets/Cell_Type_Geneset.csv

Contains the base immune gene expression signature genes and paper references. Immunity 2013 paper - https://doi.org/10.1016/j.immuni.2013.10.003 PLoS 2017 paper - https://doi.org/10.1371/journal.pone.0181868 CCR 2017 paper - 10.1158/1078-0432.CCR-17-0162