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DESCRIPTION
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DESCRIPTION
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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'