maftools is an R/Bioconductor package for the analysis and visualization of somatic mutations in cancer genomics, primarily using Mutation Annotation Format (MAF) files. It provides a comprehensive suite of functions for reading, summarizing, and plotting mutation landscapes (oncoplots, lollipop plots, rainfall plots), detecting driver genes, analyzing mutational signatures via NMF, assessing tumor heterogeneity (MATH score), comparing cohorts, and integrating copy number alterations from GISTIC or ASCAT. The package also includes tools for converting other formats (ANNOVAR, ICGC) to MAF, querying cancer hotspots directly from BAM files via a C backend, and detecting sample swaps. It is widely used by cancer researchers and relies on Bioconductor infrastructure, with extensive bundled reference data (COSMIC signatures, cancer hotspots, TCGA burden). While primarily a software library, its heavy use of precompiled research data and domain-specific pipelines gives it a hybrid character. The codebase is well-structured with S4 classes and data.table for performance, though some functions have long parameter lists and a few deprecated modules.