Introduce | Example 1 : Calculating the centrality scores of subpathways. | Example 2 : Calculating the drug-disease reverse association score and corresponding pvalue of drugs. | Visualize 1: Plot a subpathway network structure graph. | Visualize 2: Plot a heatmap of the subpathways that are regulated by disease. | Visualize 3: Plot heatmaps of the subpathways that are regulated by drugs.
Package: DRviaSPCN 0.1.5
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_0.1.5.tar.gz
DRviaSPCN_0.1.5.zip(r-4.7)DRviaSPCN_0.1.5.zip(r-4.6)DRviaSPCN_0.1.5.zip(r-4.5)
DRviaSPCN_0.1.5.tgz(r-4.6-any)DRviaSPCN_0.1.5.tgz(r-4.5-any)
DRviaSPCN_0.1.5.tar.gz(r-4.7-any)DRviaSPCN_0.1.5.tar.gz(r-4.6-any)
DRviaSPCN_0.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DRviaSPCN/json (API)
| # Install 'DRviaSPCN' in R: |
| install.packages('DRviaSPCN', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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 from:e98d94437a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 425 | ||
| source / vignettes | OK | 357 | ||
| linux-release-x86_64 | OK | 412 | ||
| macos-release-arm64 | OK | 338 | ||
| macos-oldrel-arm64 | OK | 300 | ||
| windows-devel | OK | 353 | ||
| windows-release | OK | 342 | ||
| windows-oldrel | OK | 347 | ||
| wasm-release | OK | 203 |
Exports:CalCentralityScoreDisease2SPheatmapDrug2SPheatmapgetDEscoreGetExampleOptimaldrugsPackageLoadedplotSPW
Dependencies:abindaisdkannotateAnnotationDbiapeaplotaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64blobbslibcachemcallrcliclusterclusterProfilercodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expiryDOSEdplyrenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgraphgridGraphicsGSEABasegsonGSVAgtableh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttrhttr2igraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisememusemimenlmeopensslotelpatchworkpheatmappillarpkgconfigplyrpngpolyclipprocessxpspurrrqvalueR6rappdirsRColorBrewerRcppreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdS4ArraysS4VectorsS7sassScaledMatrixscalesscatterpieSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 |
| Identifying the optimal drugs | Optimaldrugs |
| PackageLoaded | PackageLoaded |
| Plot subpathway network graph | plotSPW |
