Package: cTRAP 1.31.0

Nuno Saraiva-Agostinho

cTRAP: Identification of candidate causal perturbations from differential gene expression data

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Authors:Bernardo P. de Almeida [aut], Nuno Saraiva-Agostinho [aut, cre], Nuno L. Barbosa-Morais [aut, led]

cTRAP_1.31.0.tar.gz
cTRAP_1.31.0.zip(r-4.7)cTRAP_1.31.0.zip(r-4.6)cTRAP_1.31.0.zip(r-4.5)
cTRAP_1.31.0.tgz(r-4.6-any)cTRAP_1.31.0.tgz(r-4.5-any)
cTRAP_1.31.0.tar.gz(r-4.7-any)cTRAP_1.31.0.tar.gz(r-4.6-any)
cTRAP_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cTRAP/json (API)

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

Bug tracker:https://github.com/nuno-agostinho/ctrap/issues

Pkgdown/docs site:https://nuno-agostinho.github.io

On BioConductor:cTRAP-1.31.0(bioc 3.24)cTRAP-1.30.0(bioc 3.23)

differentialexpressiongeneexpressionrnaseqtranscriptomicspathwaysimmunooncologygenesetenrichmentbioconductorbioinformaticscmapgene-expressionl1000

4.28 score 8 stars 24 scripts 416 downloads 1 mentions 28 exports 145 dependencies

Last updated from:8c497c3abd. Checks:4 ERROR, 5 WARNING, 1 OK. Indexed: yes.

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bioc-checksERROR238
linux-devel-x86_64ERROR440
source / vignettesERROR353
linux-release-x86_64ERROR384
macos-release-arm64WARNING415
macos-oldrel-arm64WARNING498
windows-develWARNING636
windows-releaseWARNING571
windows-oldrelWARNING667
wasm-releaseOK198

Exports:analyseDrugSetEnrichmentconvertENSEMBLtoGeneSymbolsconvertGeneIdentifierscTRAPdownloadENCODEknockdownMetadatafilterCMapMetadatagetCMapConditionsgetCMapPerturbationTypeslaunchCMapDataLoaderlaunchDiffExprLoaderlaunchDrugSetEnrichmentAnalyserlaunchMetadataViewerlaunchResultPlotterlistExpressionDrugSensitivityAssociationloadCMapDataloadCMapZscoresloadDrugDescriptorsloadENCODEsamplesloadExpressionDrugSensitivityAssociationparseCMapIDperformDifferentialExpressionplotDrugSetEnrichmentplotTargetingDrugsVSsimilarPerturbationspredictTargetingDrugsprepareCMapPerturbationsprepareDrugSetsprepareENCODEgeneExpressionrankSimilarPerturbations

Dependencies:AnnotationDbiAnnotationHubaskpassassertthatbackportsbase64encBHbinrBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobbroombslibcachemcellrangerclicodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdir.expirydplyrDTevaluatefarverfastmapfastmatchfgseafilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggplot2ggrepelgluegtablehighcharterhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalubridatemagrittrMatrixmemoisemimeopensslotelpbapplypillarpkgconfigplyrpngprettyunitsprogresspromisespurrrqs2quantmodR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppParallelreadxlrematchreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrlistrmarkdownRSQLiteS4VectorsS7sassscalesSeqinfoshinyshinycssloaderssnowsourcetoolsstatmodstringfishstringistringrsystibbletidyrtidyselecttimechangetinytexTTRutf8vctrsviridisLitewithrxfunXMLxtablextsXVectoryamlzoo

Readme and manuals

Help Manual

Help pageTopics
Analyse drug set enrichmentanalyseDrugSetEnrichment
Cross Tabulation and Table Creationas.table.referenceComparison
Convert ENSEMBL gene identifiers to gene symbolsconvertENSEMBLtoGeneSymbols
Convert gene identifiersconvertGeneIdentifiers
cTRAP packagecTRAP-package cTRAP
Operations on 'expressionDrugSensitivityAssociation' objectsdim.expressionDrugSensitivityAssociation dimnames.expressionDrugSensitivityAssociation [.expressionDrugSensitivityAssociation
Download metadata for ENCODE knockdown experimentsdownloadENCODEknockdownMetadata
Filter CMap metadatafilterCMapMetadata
List available conditions in CMap datasetsgetCMapConditions
Get CMap perturbation typesgetCMapPerturbationTypes
Load CMap data via a visual interfacelaunchCMapDataLoader
Load differential expression data via a visual interfacelaunchDiffExprLoader
View and plot results via a visual interfacelaunchDrugSetEnrichmentAnalyser
View metadata via a visual interfacelaunchMetadataViewer
View and plot results via a visual interfacelaunchResultPlotter
List available gene expression and drug sensitivity correlation matriceslistExpressionDrugSensitivityAssociation
Load CMap dataloadCMapData
Load matrix of CMap perturbation's differential expression z-scores (optional)loadCMapZscores
Load table with drug descriptorsloadDrugDescriptors
Load ENCODE samplesloadENCODEsamples
Load gene expression and drug sensitivity correlation matrixloadExpressionDrugSensitivityAssociation
Parse CMap identifierparseCMapID
Perform differential gene expression based on ENCODE dataperformDifferentialExpression
Operations on a 'perturbationChanges' objectdim.perturbationChanges dimnames.perturbationChanges plot.perturbationChanges [.perturbationChanges
Plot data comparisonplot.referenceComparison
Plot drug set enrichmentplotDrugSetEnrichment
Plot similar perturbations against predicted targeting drugsplotTargetingDrugsVSsimilarPerturbations
Predict targeting drugspredictTargetingDrugs
Prepare CMap perturbation dataprepareCMapPerturbations
Prepare drug sets from a table with compound descriptorsprepareDrugSets
Load ENCODE gene expression dataprepareENCODEgeneExpression
Print a 'similarPerturbations' objectprint.similarPerturbations
Rank differential expression profile against CMap perturbations by similaritycompareAgainstCMap rankSimilarPerturbations