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'