psygenet2r: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

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Package to retrieve data from PsyGeNET database (www.psygenet.org) and to perform comorbidity studies with PsyGeNET's and user's data.

Author
Alba Gutierrez-Sacristan [aut], Carles Hernandez-Ferrer [cre]
Date of publication
None
Maintainer
Alba Gutierrez-Sacristan <alba.gutierrez@upf.edu>
License
MIT + file LICENSE
Version
1.6.2

View on Bioconductor

Man pages

DataGeNET.Psy-class
Class DataGeNET.Psy
enrichedPD-methods
Enrichment of a user's input (genes) in PsyGeNET's diseases.
extract
Raw data from 'DataGeNET.Psy' and 'JaccardIndexPsy'.
extractSentences
Method to obtain the evidences from a 'DataGeNET.Psy' object.
geneAttrPlot-methods
Ploting the relation between genes and disease-categories
getUMLs-methods
Query PsyGeNET for given gene(s) and generates an...
jaccardEstimation-methods
Calculation of the Jaccard Index between ideseases
JaccardIndexPsy-class
Class JaccardIndexPsy
ndisease
Getter from 'DataGeNET.Psy'.
ngene
Getter from 'DataGeNET.Psy'.
pantherGraphic-methods
Query PsyGeNET for given genes and creates a representation...
plot-DataGeNET.Psy-ANY-method
Plots the content of a 'DataGeNET.Psy' or 'JaccardIndexPsy'...
plot-JaccardIndexPsy-ANY-method
Plot the content of a 'JaccardIndexPsy' object.
psygenet2r
psygenet2r: Package to query PsyGeNET database and to perform...
psygenetDisease-methods
Query PsyGeNET for given disease(s) and generates an...
psygenetDiseaseSentences
Query PsyGeNET for given disease(s) and extract the pmids...
psygenetGene-methods
Query PsyGeNET for given gene(s) and generates an...
psygenetGeneSentences
Query PsyGeNET for given gene(s) and extract the pmids...
qr
'DataGeNET.Psy' obtained from quering PsyGeNET for gene...
topAnatEnrichment-methods
Enrichment of a user's input (genes) in anatomical terms...

Files in this package

psygenet2r/DESCRIPTION
psygenet2r/LICENSE
psygenet2r/NAMESPACE
psygenet2r/NEWS
psygenet2r/R
psygenet2r/R/0_AllClasses.R
psygenet2r/R/1_AllGenerics.R
psygenet2r/R/DataGeNET_Psy-extract.R
psygenet2r/R/DataGeNET_Psy-extractSentences.R
psygenet2r/R/DataGeNET_Psy-ndisease.R
psygenet2r/R/DataGeNET_Psy-ngene.R
psygenet2r/R/DataGeNET_Psy-plot.R
psygenet2r/R/DataGeNET_Psy-show.R
psygenet2r/R/JaccardIndexPsy-extract.R
psygenet2r/R/JaccardIndexPsy-plot.R
psygenet2r/R/JaccardIndexPsy-show.R
psygenet2r/R/ListPsyGeNETIds.R
psygenet2r/R/check_database.R
psygenet2r/R/check_genes.R
psygenet2r/R/disGeNET.R
psygenet2r/R/diseaseNameMapping.R
psygenet2r/R/enrichedPD.R
psygenet2r/R/geneAttrPlot.R
psygenet2r/R/getUMLs.R
psygenet2r/R/getUrl.R
psygenet2r/R/jaccardEstimation.R
psygenet2r/R/pantherGraphicCorrect.R
psygenet2r/R/psyGenDisId.R
psygenet2r/R/psygenet2r.R
psygenet2r/R/psygenetAll.R
psygenet2r/R/psygenetDisease.R
psygenet2r/R/psygenetDiseaseSentences.R
psygenet2r/R/psygenetGene.R
psygenet2r/R/psygenetGeneSentences.R
psygenet2r/R/qr.R
psygenet2r/R/topAnatEnrichment.R
psygenet2r/build
psygenet2r/build/vignette.rds
psygenet2r/data
psygenet2r/data/qr.rda
psygenet2r/inst
psygenet2r/inst/doc
psygenet2r/inst/doc/caseStudy.R
psygenet2r/inst/doc/caseStudy.Rnw
psygenet2r/inst/doc/caseStudy.pdf
psygenet2r/inst/doc/generalOverview.R
psygenet2r/inst/doc/generalOverview.Rnw
psygenet2r/inst/doc/generalOverview.pdf
psygenet2r/inst/extdata
psygenet2r/inst/extdata/ensemble2gene_symbol.tsv
psygenet2r/inst/extdata/psychiatricDisordersPubmed.csv
psygenet2r/inst/extdata/topAnat.RData
psygenet2r/man
psygenet2r/man/DataGeNET.Psy-class.Rd
psygenet2r/man/JaccardIndexPsy-class.Rd
psygenet2r/man/enrichedPD-methods.Rd
psygenet2r/man/extract.Rd
psygenet2r/man/extractSentences.Rd
psygenet2r/man/geneAttrPlot-methods.Rd
psygenet2r/man/getUMLs-methods.Rd
psygenet2r/man/jaccardEstimation-methods.Rd
psygenet2r/man/ndisease.Rd
psygenet2r/man/ngene.Rd
psygenet2r/man/pantherGraphic-methods.Rd
psygenet2r/man/plot-DataGeNET.Psy-ANY-method.Rd
psygenet2r/man/plot-JaccardIndexPsy-ANY-method.Rd
psygenet2r/man/psygenet2r.Rd
psygenet2r/man/psygenetDisease-methods.Rd
psygenet2r/man/psygenetDiseaseSentences.Rd
psygenet2r/man/psygenetGene-methods.Rd
psygenet2r/man/psygenetGeneSentences.Rd
psygenet2r/man/qr.Rd
psygenet2r/man/topAnatEnrichment-methods.Rd
psygenet2r/tests
psygenet2r/tests/testthat
psygenet2r/tests/testthat.R
psygenet2r/tests/testthat/test_basic_disease.R
psygenet2r/tests/testthat/test_basic_gene.R
psygenet2r/vignettes
psygenet2r/vignettes/caseStudy.Rnw
psygenet2r/vignettes/generalOverview.Rnw