Imports
SummarizedExperiment, VariantAnnotation, Biostrings, base,
methods, magrittr, tibble, tidyr, gtools, gridExtra,
MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang,
BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges,
IRanges, S4Vectors, uwot, ggplot2, stringr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels,
ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap,
philentropy, maftools, shiny, stringi, tidyverse, ggpubr,
Matrix (>= 1.6.1), scales
Suggests
TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard,
shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr,
rmarkdown, survival, XVector, qpdf, covr, shinyWidgets,
cowplot, withr