We build the sample tree from somatic mutations and visualized the tree by ggtree

add pvalue of the boxplot

easypar makes it easy to implement parallel computations in R. To use this package, you need to have a function that carries out your desired computation. easypar will take care of the burden of turning that function into a runnable parallel piece of code, offering two possible soilutions: generating a parallel function call exploiting the foreach and doParallel paradigms for parallel computing. or generating a ready-to-use array job for the popular LSF (Platform Load Sharing Facility) workload for distributed high performance computing. With easypar, speeding up R computations through parallelism is a trivial task.

TCGA MAF Data analysis

In this package, we use the ecology methods to estimate the Tumor Heterogeneity(TH) based on their mutated loci of variant allele frequencis(VAF)

Apply function family is a basic function in R. The apply function famliy includes apply, lapply, sapply, mapply and tapply.

This is from example code of R package ‘nnls’(Non-negative least square regression).