Package: goProfiles 1.75.0

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_1.75.0.tar.gz
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goProfiles_1.75.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
goProfiles/json (API)

# Install 'goProfiles' in R:

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

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-1.75.0(bioc 3.24)goProfiles-1.74.0(bioc 3.23)

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

annotation go geneexpression genesetenrichment graphandnetwork microarray multiplecomparison pathways software

5.48 score 1 packages 8 scripts 528 downloads 10 mentions 29 exports 40 dependencies

Last updated from:8569caa971. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	221
linux-devel-x86_64	NOTE	331
source / vignettes	OK	266
linux-release-x86_64	NOTE	321
macos-release-arm64	NOTE	161
macos-oldrel-arm64	NOTE	159
windows-devel	NOTE	187
windows-release	NOTE	197
windows-oldrel	NOTE	178
wasm-release	OK	155

Exports:as.GOTerms.frame as.GOTerms.list basicProfile BioCpack2EntrezIDS BioCpack2Profiles BioCprobes2Entrez compareGeneLists compareGOProfiles compareProfilesLists compSummary contractedProfile equivalentGOProfiles equivClust equivClust2pdf equivSummary expandedLevel expandedProfile expandTerm fisherGOProfiles fitGOProfile getAncestorsLst getGOLevel GOTermsFrame2GOTermsList GOTermsList iterEquivClust mergeProfilesLists ngenes plotProfiles printProfiles

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli CompQuadForm cpp11 crayon curl DBI fastmap generics glue GO.db httr IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pkgconfig png R6 rlang RSQLite S4Vectors Seqinfo stringi stringr sys vctrs XVector

goProfiles Vignette

Introduction | Requirements | Quick start | User guide | References

Rendered fromgoProfiles.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Performs Gene Ontology based analysis using Functional Profiles.	goProfiles-package goProfiles
Builds basic functional profile	basicProfile
Entrez identifiers for CD4-TCells example	CD4GOTermsFrame CD4GOTermsList CD4LLids
Ready 2 cluster equivalence distance matrix obtained from the analysis of the "Kidney Dataset" at level 2 of the MF ontology	clustKidneyMF2
Compares two lists of genes by building (expanded) profiles and comparing them	compareGeneLists
Comparison of lists of genes through their functional profiles	compareGOProfiles
Compares two of expanded profiles	compareProfilesLists
This function returns a brief summary of the comparison between two (expanded) profiles.	compSummary
Converts an expanded GO profile into a basic (contracted) GO profile	contractedProfile contractedProfile.default contractedProfile.ExpandedGOProfile
Functions to transformconvert objects between different types	as.GOTerms.frame as.GOTerms.list BioCpack2EntrezIDS BioCpack2Profiles BioCprobes2Entrez GOTermsFrame2GOTermsList
Entrez identifiers for genes related with an eye mutation in drosophila	drosophilaIds 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 levels	expandedLevel expandTerm
Builds expanded profiles	expandedProfile
GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles	fisherGOProfiles 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' identifiers	getAncestorsLst getGOLevel GOTermsList
Entrez Identifiers obtained from the Human Genome Organization	hugoIds
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 rejection	kidneyGeneLists
Combines two lists of profiles into one	mergeProfilesLists
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 database	diseaseIds dominantIds dominantIdsEBI dominantIdsNCBI morbidmapIds omimIds recessiveIds recessiveIdsEBI recessiveIdsNCBI
Plot functional profiles	plotProfiles
Print functional profiles	printProfiles
Prostate cancer-related genes	prostateIds singh01EntrezIDs singh05EntrezIDs welsh01EntrezIDs welsh05EntrezIDs