Package: hdWGCNA 0.5.00
hdWGCNA: High-dimensional Weighted Gene Co-expression Network Analysis
hdWGCNA is an R package for performing weighted gene co-expression network analysis in high dimensional -omics such as single-cell RNA-seq or spatial transcriptomics. It provides tools for constructing metacells, building co-expression networks, computing module eigengenes, and performing various downstream analyses including module trait correlation, module preservation, and transcription factor network analysis.
Authors:
hdWGCNA_0.5.00.tar.gz
hdWGCNA_0.5.00.zip(r-4.7)hdWGCNA_0.5.00.zip(r-4.6)hdWGCNA_0.5.00.zip(r-4.5)
hdWGCNA_0.5.00.tgz(r-4.6-any)hdWGCNA_0.5.00.tgz(r-4.5-any)
hdWGCNA_0.5.00.tar.gz(r-4.7-any)hdWGCNA_0.5.00.tar.gz(r-4.6-any)
hdWGCNA_0.5.00.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hdWGCNA/json (API)
| # Install 'hdWGCNA' in R: |
| install.packages('hdWGCNA', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zaoqu-liu/hdwgcna/issues
Pkgdown/docs site:https://zaoqu-liu.github.io
Last updated from:5c381c7246 (on main). Checks:7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | ERROR | 327 | ||
| source / vignettes | OK | 371 | ||
| linux-release-x86_64 | ERROR | 391 | ||
| macos-release-arm64 | ERROR | 242 | ||
| macos-oldrel-arm64 | ERROR | 410 | ||
| windows-devel | ERROR | 315 | ||
| windows-release | ERROR | 309 | ||
| windows-oldrel | ERROR | 320 | ||
| wasm-release | OK | 256 |
Exports:AssignTFRegulonsAvgModuleExprBinPseudotimeCheckSeurat5CheckWGCNANameConstructMetacellsConstructMetaspotsConstructNetworkConstructPseudobulkConstructTFNetworkcorSparseDimPlotMetacellsDoHubGeneHeatmapEnrichrBarPlotEnrichrDotPlotFindAllDMEsFindDifferentialRegulonsFindDMEsFindMajorIsoformsGetActiveWGCNAGetActiveWGCNANameGetAvgModuleExprGetDatExprGetDegreesGetEnrichrRegulonTableGetEnrichrTableGetHubGenesGetMELoadingsGetMEsGetMetacellObjectGetMetacellParamsGetModulePreservationGetModulesGetModuleScoresGetModuleTraitCorrelationGetModuleUMAPGetMotifMatrixGetMotifOverlapGetMotifsGetMotifScoresGetMotifTargetsGetMultiExprGetNetworkDataGetPFMListGetPowerTableGetRegulonScoresGetTFEvalGetTFNetworkGetTFRegulonsGetTFTargetGenesGetTOMGetWGCNAGenesGetWGCNAParamsHubGeneNetworkPlotMetacellsByGroupsMetaspotsByGroupsModuleConnectivityModuleCorrelogramModuleCorrNetworkModuleEigengenesModuleExprScoreModuleFeaturePlotModuleNetworkPlotModulePreservationModulePreservationNetRepModuleRadarPlotModuleRegulatoryHeatmapModuleRegulatoryNetworkModuleRegulatoryNetworkPlotModuleTopologyBarplotModuleTopologyHeatmapModuleTraitCorrelationModuleUMAPPlotMotifOverlapBarPlotMotifScanNormalizeMetacellsOverlapBarPlotOverlapDotPlotOverlapModulesDEGsOverlapModulesMotifsPlotDendrogramPlotDifferentialRegulonsPlotDMEsLollipopPlotDMEsVolcanoPlotKMEsPlotModulePreservationPlotModulePreservationLollipopPlotModuleTraitCorrelationPlotModuleTrajectoryPlotSoftPowersProjectModulesReassignModulesRegulonBarPlotRegulonScoresResetModuleColorsResetModuleNamesRunEnrichrRunEnrichrRegulonsRunHarmonyMetacellsRunModuleUMAPRunPCAMetacellsRunUMAPMetacellsscale01ScaleMetacellsSelectNetworkGenesSetActiveWGCNASetAvgModuleExprSetDatExprSetDegreesSetEnrichrRegulonTableSetEnrichrTableSetMELoadingsSetMEsSetMetacellObjectSetMetacellParamsSetModulePreservationSetModulesSetModuleScoresSetModuleTraitCorrelationSetModuleUMAPSetMotifMatrixSetMotifOverlapSetMotifsSetMotifScoresSetMotifTargetsSetMultiExprSetNetworkDataSetPFMListSetPowerTableSetRegulonScoresSetTFEvalSetTFNetworkSetTFRegulonsSetupForWGCNASetWGCNAGenesSetWGCNAParamsshuffle_pointsTestSoftPowersTestSoftPowersConsensusTFNetworkPlotTransferModuleGenomeumap_theme
Dependencies:abindaskpassbackportsbase64encBHBiocGenericsbitopsbslibcachemcaToolscheckmatecliclustercodetoolscolorspacecommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdoParalleldotCall64dplyrdqrngdynamicTreeCutenrichRevaluatefarverfastclusterfastDummiesfastmapfitdistrplusFNNfontawesomeforeachforeignFormulafsfuturefuture.applyGeneOverlapgenericsGenomicRangesggforceggplot2ggraphggrepelggridgesglobalsgluegoftestgplotsgraphlayoutsgridExtragtablegtoolsharmonyherehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttricaigraphimputeIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmennetopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclippreprocessCoreprogressrpromisesproxypurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulateRhpcBLASctlrjsonrlangrmarkdownROCRrpartrprojrootRSpectrarstudioapiRtsneS4VectorsS7sassscalesscattermoresctransformSeqinfoSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortestertibbletidygraphtidyrtidyselecttinytextweenrutf8uwotvctrsviridisviridisLiteWGCNAwithrWriteXLSxfunxtableyamlzoo
