Including Transition/Transversions into oncoplot | Changing colors for variant classifications | Including copy number data into oncoplots. | GISTIC results | Custom copy-number table | Bar plots | Including annotations | Highlighting samples | Group by Pathways | Oncogenic siganlling pathways | Biological processes of known drivers | Custom pathway list | Collapse pathways | Combining everything | SessionInfo

Introduction | Citation | Generating MAF files | MAF field requirements | Installation | Overview of the package | Reading and summarizing maf files | Required input files | Reading MAF files. | MAF object | Visualization | Plotting MAF summary. | Oncoplots | Drawing oncoplots | Transition and Transversions. | Lollipop plots for amino acid changes | MAF as an input | Custom data as an input | Rainfall plots | Compare mutation load against TCGA cohorts | Plotting VAF | Processing copy-number data | Reading and summarizing gistic output files. | Visualizing gistic results. | genome plot | Co-gisticChromPlot | Bubble plot | oncoplot | CBS segments | Summarizing chromosomal arm level CN | Visualizing CBS segments | Analysis | Somatic Interactions | Detecting cancer driver genes based on positional clustering | Adding and summarizing pfam domains | Survival analysis | Mutation in any given genes | Predict genesets associated with survival | Comparing two cohorts (MAFs) | Forest plots | Co-onco plots | Co-bar plots | Lollipop plot-2 | Clinical enrichment analysis | Drug-Gene Interactions | Oncogenic Signaling Pathways | Tumor heterogeneity and MATH scores | Heterogeneity in tumor samples | Ignoring variants in copy number altered regions | Mutational Signatures | APOBEC Enrichment estimation. | Differences between APOBEC enriched and non-enriched samples | Signature analysis | Variant Annotations | Converting annovar output to MAF | Converting ICGC Simple Somatic Mutation Format to MAF | Prepare MAF file for MutSigCV analysis | Set operations | Subsetting MAF | Specifying queries and controlling output fields. | Subsetting by clinical data | Sample swap identification | TCGA cohorts | Available cohorts | Loading a TCGA cohort | MultiAssayExperiment | Useful links and tools | References | Session Info | Support and acknowledgments | Github | Acknowledgements

Introduction | Van Loo P, Nordgard SH, Lingjærde OC, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A. 2010;107(39):16910-16915. doi:10.1073/pnas.1009843107 | Step-1: Get nucleotide counts for genetic markers | Step-2: Prepare input files for ASCAT with prepAscat() | Tumor-Normal pair | Tumor only | CBS segmentation | Processing Mosdepth output | Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699 | Tumor normal pair | Session Info

Genotype cancer hotspots | Fetch readcounts for targetted loci