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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("psygenet2r")
AuthorAlba Gutierrez-Sacristan [aut], Carles Hernandez-Ferrer [cre]
Bioconductor views BiomedicalInformatics DataImport DataRepresentation Genetics Infrastructure Software
Date of publicationNone
MaintainerAlba Gutierrez-Sacristan <alba.gutierrez@upf.edu>
LicenseMIT + file LICENSE
Version1.7.4

View on Bioconductor

Functions

DataGeNET.Psy-class Man page
enrichedPD Man page
extract Man page
extract,DataGeNET.Psy-method Man page
extract,JaccardIndexPsy-method Man page
extractSentences Man page
extractSentences,DataGeNET.Psy-method Man page
geneAttrPlot Man page
getUMLs Man page
jaccardEstimation Man page
JaccardIndexPsy-class Man page
ndisease Man page
ndisease,DataGeNET.Psy-method Man page
ngene Man page
ngene,DataGeNET.Psy-method Man page
pantherGraphic Man page
plot,DataGeNET.Psy,ANY-method Man page
plot,JaccardIndexPsy,ANY-method Man page
psygenet2r Man page
psygenet2r-package Man page
psygenetDisease Man page
psygenetDiseaseSentences Man page
psygenetGene Man page
psygenetGeneSentences Man page
qr Man page
topAnatEnrichment Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.