Maftools is an R Bioconductor package designed to facilitate the analysis and visualization of somatic variants in cancer genomics. It offers a variety of modules for driver gene identification, pathway analysis, signature identification, enrichment analysis, and association studies. Maftools requires only the Mutation Annotation Format (MAF) of somatic variants and does not depend on larger alignment files, making it suitable for analyzing public datasets. The package includes well-established statistical and computational methods, enabling data-driven research and comparative analysis. Using three well-annotated cohorts from The Cancer Genome Atlas (TCGA), the authors demonstrate the reproducibility of known results and the ability of Maftools to uncover novel findings through integrative analysis. Key features of Maftools include visualization options such as oncoplots, lollipop plots, and rainfall plots, as well as functions for mutational signature analysis, copy number data integration, and variant annotations.Maftools is an R Bioconductor package designed to facilitate the analysis and visualization of somatic variants in cancer genomics. It offers a variety of modules for driver gene identification, pathway analysis, signature identification, enrichment analysis, and association studies. Maftools requires only the Mutation Annotation Format (MAF) of somatic variants and does not depend on larger alignment files, making it suitable for analyzing public datasets. The package includes well-established statistical and computational methods, enabling data-driven research and comparative analysis. Using three well-annotated cohorts from The Cancer Genome Atlas (TCGA), the authors demonstrate the reproducibility of known results and the ability of Maftools to uncover novel findings through integrative analysis. Key features of Maftools include visualization options such as oncoplots, lollipop plots, and rainfall plots, as well as functions for mutational signature analysis, copy number data integration, and variant annotations.