psygenet2r: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Version 1.8.0

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

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
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("psygenet2r")

Getting started

psygenet2r: An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
psygenet2r: Case study on GWAS on bipolar disorder

Popular man pages

enrichedPD-methods: Enrichment of a user's input (genes) in PsyGeNET's diseases.
jaccardEstimation-methods: Calculation of the Jaccard Index between ideseases
JaccardIndexPsy-class: Class 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...
psygenetGene-methods: Query PsyGeNET for given gene(s) and generates an...
See all...

All man pages Function index File listing

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...

Functions

DataGeNET.Psy-class Man page
JaccardIndexPsy-class Man page
ListPsyGeNETIds Source code
category_plot Source code
check_database Source code
check_genes Source code
disGenetCurated Source code
diseaseNameMapping Source code
disgenetAll Source code
download_data Source code
enrichedPD Man page Source code
extract Man page
extract,DataGeNET.Psy-method Man page
extract,JaccardIndexPsy-method Man page
extractSentences Man page
extractSentences,DataGeNET.Psy-method Man page
freq_function Source code
freq_functionAll Source code
geneAttrPlot Man page Source code
gene_plot Source code
getDiseasesType Source code
getUMLs Man page Source code
getUrlDis Source code
getUrlPsi Source code
jaccardEstimation Man page Source code
ji.internal Source code
multipleInput Source code
ndex_plot Source code
ndisease Man page
ndisease,DataGeNET.Psy-method Man page
ngene Man page
ngene,DataGeNET.Psy-method Man page
pantherGraphic Man page Source code
pie_plot Source code
plot,DataGeNET.Psy,ANY-method Man page
plot,JaccardIndexPsy,ANY-method Man page
plot_datagenet_psy Source code
plot_pmids_barplot Source code
plot_psy_disease Source code
plot_psy_heatmap Source code
plot_psy_heatmapDisease Source code
plot_psy_heatmapGenes Source code
plot_psy_heatmapScore Source code
plot_psy_psychiatric Source code
psyGenDisId Source code
psyPanther Source code
psygenet2r Man page
psygenet2r-package Man page
psygenetAll Source code
psygenetDisease Man page Source code
psygenetDiseaseSentences Man page Source code
psygenetGene Man page Source code
psygenetGeneSentences Man page Source code
qr Man page
singleInput Source code
singleInput.genes Source code
topAnatEnrichment Man page Source code
transPantherFile Source code

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/general_overview.Rmd
vignettes/general_overview.bib
psygenet2r documentation built on May 20, 2017, 10:44 p.m.