R code for paper "Immuno-transcriptomic profiling of extracranial pediatric solid malignancies" https://www.sciencedirect.com/science/article/pii/S2211124721015333
Brohl, A. S., Sindiri, S., Wei, J. S., Milewski, D., Chou, H. C., Song, Y. K., ... & Khan, J. (2021). Immuno-transcriptomic profiling of extracranial pediatric solid malignancies. Cell reports, 37(8), 110047.
The easiest way to get this script is to clone the repository.
SSH:
git clone [email protected]:CCRGeneticsBranch/RNAseqLandscape.git
HTTPS:
https://github.com/CCRGeneticsBranch/RNAseqLandscape.git
We need an extra data file (too large for GitHub). Please copy this to input/GeneRDS/:
cp /data/khanlab3/hsienchao/Landscape/RPKM_Data_Filt_Consolidated.GeneNames.all.TCGA.Khanlab.pc.log22019-03-19.rds RNAseqLandscape/input/GeneRDS/
We need the following R packages. Please make sure they are installed properly:
plyr
dplyr
data.table
ggplot2
tidyr
gridExtra
ggrepel
RColorBrewer
treemap
lazyeval
grid
ggridges
scales
randomcoloR
gplots
pheatmap
ape
amap
limma
edgeR
psych
tibble
Hmisc
Please change directory to the cloned folder:
cd RNAseqLandscape
Then run:
Rscript src/expressionAnalysis.R
You might see many warnings but they will not affect the results. This script has been tested in R 4.0.
output/Figures: all the figures
output/FigureData: the data used to generate figures
output/DiffExpResults: the output of differential expression analyses
output/MiXCR: the output data for TCR analysis