Package: MOSClip 1.1.0
Paolo Martini
MOSClip: Multi Omics Survival Clip
Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.
Authors:
MOSClip_1.1.0.tar.gz
MOSClip_1.1.0.zip(r-4.5)MOSClip_1.1.0.zip(r-4.4)
MOSClip_1.1.0.tgz(r-4.4-any)
MOSClip_1.1.0.tar.gz(r-4.5-noble)MOSClip_1.1.0.tar.gz(r-4.4-noble)
MOSClip_1.1.0.tgz(r-4.4-emscripten)
MOSClip.pdf |MOSClip.html✨
MOSClip/json (API)
NEWS
# Install 'MOSClip' in R: |
install.packages('MOSClip', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/caluralab/mosclip/issues
- multiOmics - Omics class object with TCGA ovarian data
- multiOmicsTopo - Omics class object with TCGA ovarian data for topological analysis
- ovarianDataset - ExperimentList class object with TCGA ovarian data
- reactSmall - PathwayList of pathways from Reactome
On BioConductor:MOSClip-0.99.5(bioc 3.20)
softwarestatisticalmethodgraphandnetworksurvivalregressiondimensionreductionpathwaysreactome
Last updated 2 days agofrom:412bda8a84. Checks:OK: 3 NOTE: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 30 2024 |
R-4.5-win | NOTE | Oct 31 2024 |
R-4.5-linux | NOTE | Oct 30 2024 |
R-4.4-win | OK | Oct 31 2024 |
R-4.4-mac | OK | Oct 31 2024 |
Exports:addResamplingCountsannotePathwayToFatheravailableOmicMethodscomputeFreqscomputeOmicsIntersectionsdownloadPathwayRelationFromReactomegetPathwaysModulesSuccessmakeOmicsmultiOmicsSurvivalModuleTestmultiOmicsSurvivalPathwayTestmultiOmicsTwoClassModuleTestmultiOmicsTwoClassPathwayTestmultiPathwayModuleReportmultiPathwayReportplotFrequenciesplotModuleHeatplotModuleInGraphplotModuleKMplotModuleReportplotMultiPathwayReportplotPathwayHeatplotPathwayKMresamplingModulesSurvivalresamplingModulesTwoClassresamplingPathwaySurvivalresamplingPathwayTwoClassrunSupertestselectStablePathwaysModulesshowModuleshowMOSpaletteshowOmicsshowPathwaystripModulesFromPathways
Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacheckmatecirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcorpcorcorrplotcowplotcoxrobustcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDerivdigestdoBydoParalleldplyrDTelasticnetellipseemmeansestimabilityevaluateexactRankTestsFactoMineRfansifarverfastmapflashClustfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggplotifyggpubrggrepelggsciggsignifggtextGlobalOptionsgluegraphgraphitegRbasegridExtragridGraphicsgridtextgtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTkm.ciKMsurvknitrlabelinglambda.rlarslaterlatticelazyevalleapslifecyclelme4magrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewMultiAssayExperimentmunsellmvtnormNbClustnlmenloptrnnetnumDerivopensslorg.Hs.eg.dbpbkrtestpheatmappillarpkgconfigplogrplyrpngpolynompromisespurrrqpgraphqtlquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshaperestfulrRgraphvizRhtslibrjsonrlangrmarkdownRsamtoolsRSQLiterstatixrtracklayerS4ArraysS4Vectorssassscalesscatterplot3dshapesnowSparseArraySparseMstringistringrSummarizedExperimentSuperExactTestsurvivalsurvminersurvMiscsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryamlyulab.utilszlibbioczoo