Package: gep2pep 1.25.0

Francesco Napolitano

gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.

Authors:Francesco Napolitano <[email protected]>

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gep2pep.pdf |gep2pep.html✨
gep2pep/json (API)
NEWS

# Install 'gep2pep' in R:
install.packages('gep2pep', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:gep2pep-1.25.0(bioc 3.20)gep2pep-1.24.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

25 exports 0.61 score 51 dependencies 3 mentions

Last updated 2 months agofrom:45570c71d9

Exports:addSingleGeneSetsas.CategorizedCollectionbuildPEPsCategorizedCollectioncheckRepositoryclearCacheCondSEAcreateMergedRepositorycreateRepositoryexportSEAgene2pathwaysgetCollectionsgetDetailsgetResultsimportFromRawModeimportMSigDB.xmlloadCollectionloadESmatrixloadPVmatrixloadSampleGEPloadSamplePWSmakeCollectionIDsopenRepositoryPathSEAsetId2setName

Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdigestfastmapforeachGenomeInfoDbGenomeInfoDbDatagluegraphGSEABasehttrIRangesiteratorsjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6reporhdf5rhdf5filtersRhdf5librlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

Introduction to gep2pep

Francesco Napolitano

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-02-16
Started: 2017-09-10

Readme and manuals

Help Manual

Help pageTopics
gep2pep: creation and analysis of Pathway Expression Profilesgep2pep-package gep2pep
Adds a collection of single-gene psuedo-sets.addSingleGeneSets
Converts GeneSetCollection objects to CategorizedCollection objects.as.CategorizedCollection
Build PEPs from GEPs and stores them in the repository.buildPEPs
Constructor method for objects of class CategorizedCollection.CategorizedCollection
A class to contain categorized gene set collectionCategorizedCollection-class
Check an existyng repository for consistencycheckRepository
Clear cached ranked matricesclearCache
Performs Condition Set Enrichment AnalysisCondSEA
Merge multiple PEPs to build a repository of consensus PEPscreateMergedRepository
Creates a repository of pathway collections.createRepository
Export CondSEA or PathSEA results to XLS formatexportSEA
Finds pathways including a given gene.gene2pathways
Returns the names of the pathway collections in a repository.getCollections
Extracts the details matrix from 'CondSEA' or 'PathSEA' outputgetDetails
Extracts the results matrix from 'CondSEA' or 'PathSEA' outputgetResults
Imports PEPs created in raw modeimportFromRawMode
Imports pathways data from an MSigDB XML file.importMSigDB.xml
Loads a collection of pathways from the repositoryloadCollection
Loads the matrix of Enrichment Scores for a collectionloadESmatrix
Loads the matrix of p-values for a collectionloadPVmatrix
Loads sample Gene Expression ProfilesloadSampleGEP
Loads sample pathway collectionsloadSamplePWS
Creates a collection label for each pathway.makeCollectionIDs
Opens an existing repository of pathway collections.openRepository
Performs Pathway Set Enrichment Analysis (PSEA)PathSEA
Converts gene set IDs to gene set namessetId2setName