Introduction | A Simple Example | Importing Data | Normalisation | Calculating Differential Expression | Selecting Ranked Lists | Classifying Profiles
Package: DrugVsDisease 2.55.0
j. Saez-Rodriguez
DrugVsDisease: Comparison of disease and drug profiles using Gene set Enrichment Analysis
This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.
Authors:
DrugVsDisease_2.55.0.tar.gz
DrugVsDisease_2.55.0.zip(r-4.7)DrugVsDisease_2.55.0.zip(r-4.6)DrugVsDisease_2.55.0.zip(r-4.5)
DrugVsDisease_2.55.0.tgz(r-4.6-any)DrugVsDisease_2.55.0.tgz(r-4.5-any)
DrugVsDisease_2.55.0.tar.gz(r-4.7-any)DrugVsDisease_2.55.0.tar.gz(r-4.6-any)
DrugVsDisease_2.55.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DrugVsDisease/json (API)
| # Install 'DrugVsDisease' in R: |
| install.packages('DrugVsDisease', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- customClust - Custom Clusters
- customDB - Custom Gene Expression Profiles
- customedge - Edge attributes for example custom network
- customsif - SIF file for custom clusters
- profiles - Gene Expression Profiles
- selprofile - List: Differential gene expression and p-values
On BioConductor:DrugVsDisease-2.55.0(bioc 3.24)DrugVsDisease-2.54.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraygeneexpressionclustering
Last updated from:04ae45238e. Checks:3 ERROR, 5 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 245 | ||
| linux-devel-x86_64 | NOTE | 384 | ||
| source / vignettes | OK | 309 | ||
| linux-release-x86_64 | NOTE | 345 | ||
| macos-release-arm64 | ERROR | 262 | ||
| macos-oldrel-arm64 | ERROR | 175 | ||
| windows-devel | NOTE | 238 | ||
| windows-release | NOTE | 237 | ||
| windows-oldrel | NOTE | 259 | ||
| wasm-release | OK | 235 |
Exports:classifyprofilecombineProfilesgenerateprofilesselectrankedlists
Dependencies:abindaffxparseraffyaffyioannotateAnnotationDbiArrayExpressaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerbiomaRtBiostringsbitbit64blobcachemclicliprcMap2datacodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrDrugVsDiseasedatafarverfastmapfffilelockforeachgenericsGenomicRangesGEOqueryggplot2gluegtablehgu133a.dbhgu133a2.dbhgu133plus2.dbhmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeoligooligoClassesopensslorg.Hs.eg.dbpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrentrezreshape2rlangRSQLiteRUnitrvestS4ArraysS4VectorsS7scalesselectrSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DrugVsDisease Package Overview | DrugVsDisease-package DrugVsDisease |
| Classify Profiles | classifyprofile |
| Combine Profiles | combineProfiles |
| Custom Clusters | customClust |
| Custom Gene Expression Profiles | customDB |
| Edge attributes for example custom network | customedge |
| SIF file for custom clusters | customsif |
| Generate Profiles | generateprofiles |
| Gene Expression Profiles | profiles |
| Select Ranked Lists | selectrankedlists |
| List: Differential gene expression and p-values | selprofile |