Package: signeR
Type: Package
Title: Empirical Bayesian approach to mutational signature discovery
Version: 2.13.0
Author: Rafael Rosales, Rodrigo Drummond, Renan Valieris, Alexandre
        Defelicibus, Israel Tojal da Silva
Maintainer: Renan Valieris <renan.valieris@accamargo.org.br>
Description: The signeR package provides an empirical Bayesian approach
        to mutational signature discovery. It is designed to analyze
        single nucleotide variation (SNV) counts in cancer genomes, but
        can also be applied to other features as well. Functionalities
        to characterize signatures or genome samples according to
        exposure patterns are also provided.
License: GPL-3
Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb,
        GenomicRanges, IRanges, nloptr, methods, stats, utils,
        PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat,
        future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada,
        future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv,
        reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble,
        readr, shiny, shinydashboard, shinycssloaders, shinyWidgets,
        bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer,
        BSgenome, broom, VariantAnnotation
Depends: R (>= 4.1.0), NMF
LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100)
SystemRequirements: C++14
URL: https://github.com/TojalLab/signeR
LazyData: true
NeedsCompilation: yes
ByteCompile: TRUE
biocViews: GenomicVariation, SomaticMutation, StatisticalMethod,
        Visualization
Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Encoding: UTF-8
Config/pak/sysreqs: cmake libglpk-dev libgmp3-dev make libbz2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libxml2-dev
        libmpfr-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:34:16 UTC
RemoteUrl: https://github.com/bioc/signeR
RemoteRef: HEAD
RemoteSha: 54b8b4dd8461823e6e1c90dca6847996e77f0cbe
Packaged: 2025-11-04 07:26:02 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2025-11-04 07:31:37 UTC; windows
Archs: x64
