MAF Wiz: A tool for visualizing MAF files

Maf Wiz like math wiz

Shiny app for plotting data from MAF files

Mutation Annotation Format (MAF) files are used for storing somatic mutation data across cohorts. For example, The Cancer Genome Atlas (TCGA) project has made MAF files from each project publicly available. This app is intended to help allow quick summarization and visualization of these kind of data.

How to run

Install R and RStudio

Here's an installation guide if you don't have these already.

Install Required Packages

list.of.packages <- c("shiny","shinyjs","openxlsx","shinycssloaders","shinyWidgets","shinythemes","RColorBrewer","ggplot2","reshape2","colourpicker")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

list.of.bioc.packages <- c("maftools","ComplexHeatmap","circlize","dplyr","ggbeeswarm","TCGAbiolinks","NMF","MutationalPatterns","BSgenome.Hsapiens.UCSC.hg38","BSgenome.Hsapiens.UCSC.hg19")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
new.bioc.packages <- list.of.bioc.packages[!(list.of.bioc.packages %in% installed.packages()[,"Package"])]
if(length(new.bioc.packages)) BiocManager::install(new.bioc.packages)

Run from GitHub in RStudio

library(shiny)
runGitHub( "mafwiz", "mtandon09", ref="dev")

Example usage:

Upload your own MAF file or download TCGA MAFs on-the-fly Add sample information for annotations Visualizations

• Mutational Burden
• Oncoplot
• Mutational Signatures (COSMIC v3)
• Output data as table

To Do

• Buncha stuff