Package: goProfiles 1.69.0

Alex Sanchez

goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.

Authors:Alex Sanchez, Jordi Ocana and Miquel Salicru

goProfiles_1.69.0.tar.gz
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goProfiles.pdf |goProfiles.html✨
goProfiles/json (API)

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

Peer review:

Datasets:
  • CD4LLids - Entrez identifiers for CD4-TCells example
  • clustKidneyMF2 - Ready 2 cluster equivalence distance matrix obtained from the analysis of the "Kidney Dataset" at level 2 of the MF ontology
  • diseaseIds - Entrez identifiers for disease-related genes in the OMIM database
  • dominantIds - Entrez identifiers for disease-related genes in the OMIM database
  • dominantIdsEBI - Entrez identifiers for disease-related genes in the OMIM database
  • dominantIdsNCBI - Entrez identifiers for disease-related genes in the OMIM database
  • drosophilaIds - Entrez identifiers for genes related with an eye mutation in drosophila
  • hugoIds - Entrez Identifiers obtained from the Human Genome Organization
  • kidneyGeneLists - Gene-lists related to kidney transplantation rejection
  • michaudIds - Entrez identifiers for genes related with an eye mutation in drosophila
  • morbidmapIds - Entrez identifiers for disease-related genes in the OMIM database
  • ostrinIds - Entrez identifiers for genes related with an eye mutation in drosophila
  • recessiveIds - Entrez identifiers for disease-related genes in the OMIM database
  • recessiveIdsEBI - Entrez identifiers for disease-related genes in the OMIM database
  • recessiveIdsNCBI - Entrez identifiers for disease-related genes in the OMIM database
  • singh01EntrezIDs - Prostate cancer-related genes
  • singh05EntrezIDs - Prostate cancer-related genes
  • welsh01EntrezIDs - Prostate cancer-related genes
  • welsh05EntrezIDs - Prostate cancer-related genes

On BioConductor:goProfiles-1.69.0(bioc 3.21)goProfiles-1.68.0(bioc 3.20)

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

annotationgogeneexpressiongenesetenrichmentgraphandnetworkmicroarraymultiplecomparisonpathwayssoftware

5.48 score 1 packages 6 scripts 358 downloads 10 mentions 29 exports 44 dependencies

Last updated 2 months agofrom:9437379f78. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:as.GOTerms.frameas.GOTerms.listbasicProfileBioCpack2EntrezIDSBioCpack2ProfilesBioCprobes2EntrezcompareGeneListscompareGOProfilescompareProfilesListscompSummarycontractedProfileequivalentGOProfilesequivClustequivClust2pdfequivSummaryexpandedLevelexpandedProfileexpandTermfisherGOProfilesfitGOProfilegetAncestorsLstgetGOLevelGOTermsFrame2GOTermsListGOTermsListiterEquivClustmergeProfilesListsngenesplotProfilesprintProfiles

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcliCompQuadFormcpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDataglueGO.dbhttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorsstringistringrsysUCSC.utilsvctrsXVectorzlibbioc

goProfiles Vignette

Rendered fromgoProfiles.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2018-04-17
Started: 2017-10-17

Readme and manuals

Help Manual

Help pageTopics
Performs Gene Ontology based analysis using Functional Profiles.goProfiles-package goProfiles
Builds basic functional profilebasicProfile
Entrez identifiers for CD4-TCells exampleCD4GOTermsFrame CD4GOTermsList CD4LLids
Ready 2 cluster equivalence distance matrix obtained from the analysis of the "Kidney Dataset" at level 2 of the MF ontologyclustKidneyMF2
Compares two lists of genes by building (expanded) profiles and comparing themcompareGeneLists
Comparison of lists of genes through their functional profilescompareGOProfiles
Compares two of expanded profilescompareProfilesLists
This function returns a brief summary of the comparison between two (expanded) profiles.compSummary
Converts an expanded GO profile into a basic (contracted) GO profilecontractedProfile contractedProfile.default contractedProfile.ExpandedGOProfile
Functions to transformconvert objects between different typesas.GOTerms.frame as.GOTerms.list BioCpack2EntrezIDS BioCpack2Profiles BioCprobes2Entrez GOTermsFrame2GOTermsList
Entrez identifiers for genes related with an eye mutation in drosophiladrosophilaIds michaudIds ostrinIds
Are two lists of genes equivalent in terms of their Gene Ontology profiles?equivalentGOProfiles equivalentGOProfiles.default equivalentGOProfiles.ExpandedGOProfile equivalentGOProfiles.GOProfileHtest
For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold distance matrix and generate a dendrogram from it.equivClust
Save the graphical representation of objects of class 'equivClust' or 'iterEquivClust' as pdf files.equivClust2pdf equivClust2pdf.equivClust equivClust2pdf.iterEquivClust
This function returns a brief summary of the equivalence test between two profiles.equivSummary
Function to create expanded levels which can contain GO Terms at different GO levelsexpandedLevel expandTerm
Builds expanded profilesexpandedProfile
GO Class-by-class Fisher tests in lists of genes characterized by their functional profilesfisherGOProfiles fisherGOProfiles.BasicGOProfile fisherGOProfiles.ExpandedGOProfile fisherGOProfiles.matrix fisherGOProfiles.numeric
Does a "sample" GO profile 'pn', observed in a sample of 'n' genes, fit a "population" or "model" p0?fitGOProfile
Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiersgetAncestorsLst getGOLevel GOTermsList
Entrez Identifiers obtained from the Human Genome OrganizationhugoIds
For each combination of the specified levels in the choosen GO ontologies, compute the equivalence threshold distance matrix and generate a dendrogram from it.iterEquivClust
Gene-lists related to kidney transplantation rejectionkidneyGeneLists
Combines two lists of profiles into onemergeProfilesLists
Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them)ngenes ngenes.BasicGOProfile ngenes.default ngenes.ExpandedGOProfile ngenes.matrix ngenes.numeric
Entrez identifiers for disease-related genes in the OMIM databasediseaseIds dominantIds dominantIdsEBI dominantIdsNCBI morbidmapIds omimIds recessiveIds recessiveIdsEBI recessiveIdsNCBI
Plot functional profilesplotProfiles
Print functional profilesprintProfiles
Prostate cancer-related genesprostateIds singh01EntrezIDs singh05EntrezIDs welsh01EntrezIDs welsh05EntrezIDs