Introduction | Identifying drug-regulated subpathways | Infer patient-specific subpathway activity profiles. | Calculating drug-disease reverse association score. | Identifying cancer subtype-specific drugs | Calculating the cancer subtype-specific drug score | Estimating statistically significance level of sutype-specific drug score | Visualization | Plot a heat map of normalized drug-disease reverse association scores for cancer samples | Plot heat map of patient-specific subpathway activity profiles of drug-regulated subpathway | Plot a global graph of the drug | Polt a subpathway network graph | Visualize the chemical structure of the drug | References
Package: SubtypeDrug 0.1.6
SubtypeDrug: Prioritization of Candidate Cancer Subtype Specific Drugs
A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype. The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
Authors:
SubtypeDrug_0.1.6.tar.gz
SubtypeDrug_0.1.6.zip(r-4.7)SubtypeDrug_0.1.6.zip(r-4.6)SubtypeDrug_0.1.6.zip(r-4.5)
SubtypeDrug_0.1.6.tgz(r-4.6-any)SubtypeDrug_0.1.6.tgz(r-4.5-any)
SubtypeDrug_0.1.6.tar.gz(r-4.7-any)SubtypeDrug_0.1.6.tar.gz(r-4.6-any)
SubtypeDrug_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SubtypeDrug/json (API)
| # Install 'SubtypeDrug' in R: |
| install.packages('SubtypeDrug', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hanjunwei-lab/subtypedrug/issues
Datasets:
- Colork - Color
- Disease_drugs - Simulated result data
- Drugs_CID - Correspondence table of drug label and drug ID in PubCham database
- Geneexp - Simulated gene expression data
- GeneexpT - Gene expression data for testing
- SpwNetworkData - Subpathway network structure data
- Subtype_drugs - Simulation result data
- UserDS - Simulated user-defined drug regulator subpathway dataset
- UserDST - User-defined drug regulator subpathway dataset for testing
- UserGS - Simulated user-defined gene set data
- UserGST - User-defined gene set data for testing
Last updated from:4bd48f9b19. Checks:8 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | ERROR | 393 | ||
| source / vignettes | ERROR | 344 | ||
| linux-release-x86_64 | ERROR | 383 | ||
| macos-release-arm64 | ERROR | 194 | ||
| macos-oldrel-arm64 | ERROR | 213 | ||
| windows-devel | ERROR | 318 | ||
| windows-release | ERROR | 283 | ||
| windows-oldrel | ERROR | 309 | ||
| wasm-release | OK | 219 |
Exports:AccumulateNormalCalculateSESgetDrugMatrixgetDrugSpwgetDrugStructureisPackageLoadedplotDScoreHeatmapplotDSpwHeatmapplotGlobalGraphplotSpwNetGraphPrioSubtypeDrugReadClsFile
Dependencies:abindannotateAnnotationDbiaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64bitopsblobbslibcachemChemmineRclicodetoolscpp11crayoncrosstalkcurlDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydplyrDTevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegraphgridExtraGSEABaseGSVAgtableh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttrhttr2igraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisememusemimeopensslotelpheatmappillarpkgconfigpngpromisespurrrR6rappdirsRColorBrewerRcppRCurlrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdrsvgrvestS4ArraysS4VectorsS7sassScaledMatrixscalesselectrSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryaml
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs
Last update: 2021-01-22
Started: 2021-01-22
