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:Xudong Han, Junwei Han, Chonghui Liu

SubtypeDrug_0.1.6.tar.gz
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SubtypeDrug.pdf |SubtypeDrug.html✨
SubtypeDrug/json (API)

# Install 'SubtypeDrug' in R:
install.packages('SubtypeDrug', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On CRAN:

12 exports 2 stars 0.94 score 140 dependencies 3 scripts 278 downloads

Last updated 8 months agofrom:4bd48f9b19. Checks:ERROR: 5 NOTE: 1 OK: 1. Indexed: yes.

TargetResultDate
Doc / VignettesFAILAug 30 2024
R-4.5-winERRORAug 30 2024
R-4.5-linuxERRORAug 30 2024
R-4.4-winERRORAug 30 2024
R-4.4-macERRORAug 30 2024
R-4.3-winOKJul 31 2024
R-4.3-macNOTEJul 31 2024

Exports:AccumulateNormalCalculateSESgetDrugMatrixgetDrugSpwgetDrugStructureisPackageLoadedplotDScoreHeatmapplotDSpwHeatmapplotGlobalGraphplotSpwNetGraphPrioSubtypeDrugReadClsFile

Dependencies:abindannotateAnnotationDbiaskpassbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64bitopsblobbslibcachemChemmineRclicodetoolscolorspacecpp11crayoncrosstalkcurlDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphgridExtraGSEABaseGSVAgtableHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplogrpngpromisespurrrR6rappdirsRColorBrewerRcppRCurlrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdrsvgrvestS4ArraysS4VectorssassScaledMatrixscalesselectrSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioc

SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs

Xudong HanJunwei HanChonghui Liu

Rendered fromvignette.Rmdusingknitr::rmarkdownon Aug 30 2024.

Last update: 2021-01-22
Started: 2021-01-22