This repository contains R scripts used for our publication "A kinase-deficient NTRK2 splice variant predominates in glioma and amplifies several oncogenic signaling pathways"

1. Vivian J, Rao AA, Nothaft FA, et al. (2017) Toil enables reproducible, open source, big biomedical data analyses. Nature biotechnology.
2. The GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. (2013) Nature genetics.
3. R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

All our analysis is done in R using the following R/Biocondcutor packages.

1. ggplot2 for making most of the plots in our paper.
2. pheatmap and RColorBrewer for making heatmaps
3. DGCA for Differential gene correlation analysis
4. edgeR and DESeq2 for finding differentially expressed genes.
5. clusterProfiler and ReactomePA for GO and pathway enrichment analysis

To ensure smooth execution of code in this repository, please install the following packages

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("DGCA", "edgeR", "DESeq2", 
                       "clusterProfiler",  "ReactomePA",
                       "pheatmap", "RColorBrewer", "ggplot2", "gridExtra"))