109 lines (108 with data), 2.4 kB

Package: MOVICS
Title: Multi-Omics integration and VIsualization in Cancer Subtyping
Version: 0.99.17
Authors@R: 
    person(given = "Xiaofan",
           family = "Lu",
           role = c("aut", "cre"),
           email = "xlu.cpu@foxmail.com",
           comment = c(ORCID = "0000-0003-2417-6548"))
Description: This package provides a unified interface for 10 state-of-the-art multi-omics clustering algorithms, and forms a pipeline for most commonly used downstream analyses in cancer subtyping researches and to create feature rich customizable visualzations with minimal effort.
Depends: R (>= 4.0.1)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: 
    testthat,
    knitr,
    rmarkdown,
    kableExtra
Remotes: 
    github::maxconway/SNFtool@master, github::danro9685/CIMLR@R, github::Lothelab/CMScaller@master, github::davidgohel/officer@master
Imports: 
    CIMLR,
    ClassDiscovery,
    ConsensusClusterPlus,
    IntNMF,
    PINSPlus,
    SNFtool,
    coca,
    dplyr,
    ggplot2,
    iClusterPlus,
    mogsa,
    vegan,
    circlize,
    survival,
    survminer,
    ggpp,
    tibble,
    limma,
    DESeq2,
    edgeR,
    aricode,
    ggalluvial,
    flexclust,
    reshape2,
    clusterProfiler,
    GSVA,
    grid,
    cowplot,
    jstable,
    impute,
    CMScaller,
    car,
    genefilter,
    ggpubr,
    preprocessCore,
    ridge,
    sva,
    grDevices,
    maftools,
    patchwork,
    ComplexHeatmap (>= 2.5.5),
    pamr,
    clusterRepro,
    officer
VignetteBuilder: knitr
RoxygenNote: 7.1.1
biocViews: Clustering, DifferentialExpression, GeneSetEnrichment, MultipleComparison, SomaticMutation, CopyNumberVariation, Survival
URL: https://github.com/xlucpu/MOVICS
BugReports: https://github.com/xlucpu/MOVICS/issues
Collate: 
    'compAgree.R'
    'compClinvar.R'
    'compDrugsen.R'
    'compFGA.R'
    'compMut.R'
    'compSurv.R'
    'compTMB.R'
    'getCIMLR.R'
    'getCOCA.R'
    'getClustNum.R'
    'getConsensusClustering.R'
    'getConsensusMOIC.R'
    'getSilhouette.R'
    'getElites.R'
    'getIntNMF.R'
    'getLRAcluster.R'
    'getMOIC.R'
    'getMoCluster.R'
    'getMoHeatmap.R'
    'getNEMO.R'
    'getPINSPlus.R'
    'getSNF.R'
    'getStdiz.R'
    'getiClusterBayes.R'
    'runDEA.R'
    'runGSEA.R'
    'runGSVA.R'
    'runMarker.R'
    'runNTP.R'
  	'runPAM.R'
  	'runKappa.R'
    'pRRophetic.R'
    'LRAcluster.R'
    'quiet.R'
    'dataset.R'
    'global.R'