Package: DRviaSPCN 0.1.4
DRviaSPCN: Drug Repurposing in Cancer via a Subpathway Crosstalk Network
A systematic biology tool was developed to repurpose drugs via a subpathway crosstalk network. The operation modes include 1) calculating centrality scores of SPs in the context of gene expression data to reflect the influence of SP crosstalk, 2) evaluating drug-disease reverse association based on disease- and drug-induced SPs weighted by the SP crosstalk, 3) identifying cancer candidate drugs through perturbation analysis. There are also several functions used to visualize the results.
Authors:
DRviaSPCN_0.1.4.tar.gz
DRviaSPCN_0.1.4.zip(r-4.5)DRviaSPCN_0.1.4.zip(r-4.4)DRviaSPCN_0.1.4.zip(r-4.3)
DRviaSPCN_0.1.4.tgz(r-4.4-any)DRviaSPCN_0.1.4.tgz(r-4.3-any)
DRviaSPCN_0.1.4.tar.gz(r-4.5-noble)DRviaSPCN_0.1.4.tar.gz(r-4.4-noble)
DRviaSPCN_0.1.4.tgz(r-4.4-emscripten)DRviaSPCN_0.1.4.tgz(r-4.3-emscripten)
DRviaSPCN.pdf |DRviaSPCN.html✨
DRviaSPCN/json (API)
| # Install 'DRviaSPCN' in R: |
| install.packages('DRviaSPCN', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
- envData - An environment variable which includes some example data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 months agofrom:8d2b8e2e81. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win | OK | Sep 12 2024 |
| R-4.5-linux | OK | Sep 12 2024 |
| R-4.4-win | OK | Sep 12 2024 |
| R-4.4-mac | OK | Sep 12 2024 |
| R-4.3-win | OK | Aug 11 2024 |
| R-4.3-mac | OK | Aug 11 2024 |
Exports:CalCentralityScoreDisease2SPheatmapDrug2SPheatmapgetDEscoreGetExamplegetMolecularFmOptimaldrugsPackageLoadedplotSPW
Dependencies:abindannotateAnnotationDbiapeaplotaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64bitopsblobbslibcachemChemmineRcliclusterProfilercodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestDOSEdplyrDTenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbGOSemSimgraphgraphlayoutsgridExtragridGraphicsGSEABasegsonGSVAgtableHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpheatmappillarpkgconfigplogrplyrpngpolyclippromisespurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdrsvgS4ArraysS4VectorssassScaledMatrixscalesscatterpieshadowtextSingleCellExperimentsnowspSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The DRviaSPCN package | DRviaSPCN-package DRviaSPCN |
| Calculating eigenvector centrality of subpathways | CalCentralityScore |
| Plot a heat map of the subpathways activity regulated by disease | Disease2SPheatmap |
| Plot a heat map of the subpathways activity regulated by drugs | Drug2SPheatmap |
| An environment variable which includes some example data | envData |
| Calculating Log2 Fold Change of genes | getDEscore |
| Get example data | GetExample |
| Plot chemical molecular formula of drugs | getMolecularFm |
| Identifying the optimal drugs | Optimaldrugs |
| PackageLoaded | PackageLoaded |
| Plot subpathway network graph | plotSPW |
