Package: psygenet2r 1.37.0

Alba Gutierrez-Sacristan

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.

Authors:Alba Gutierrez-Sacristan [aut, cre], Carles Hernandez-Ferrer [aut], Jaun R. Gonzalez [aut], Laura I. Furlong [aut]

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psygenet2r.pdf |psygenet2r.html✨
psygenet2r/json (API)
NEWS

# Install 'psygenet2r' in R:

install.packages('psygenet2r', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

qr - 'DataGeNET.Psy' obtained from quering PsyGeNET for gene '4852'.
universe - Vector with gene universe for Jaccard Index

On BioConductor:psygenet2r-1.37.0(bioc 3.20)psygenet2r-1.36.0(bioc 3.19)

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

bioconductor-package

15 exports 1.08 score 93 dependencies 2 mentions

Last updated 2 months agofrom:4240a612db

Exports:enrichedPD extract extractSentences geneAttrPlot getUMLs jaccardEstimation ndisease ngene pantherGraphic plot psygenetDisease psygenetDiseaseSentences psygenetGene psygenetGeneSentences topAnatEnrichment

Dependencies:AnnotationDbi askpass BgeeDB Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 bitops blob cachem cli colorspace cpp11 crayon curl data.table DBI dbplyr digest dplyr fansi farver fastmap filelock generics GenomeInfoDb GenomeInfoDbData ggplot2 glue GO.db graph gtable hms httr httr2 igraph IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl reshape2 rlang RSQLite S4Vectors scales SparseM stringi stringr sys tibble tidyr tidyselect topGO UCSC.utils utf8 vctrs viridisLite withr xml2 XVector zlibbioc

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

Alba Gutierrez-Sacristan, Carles Hernandez-Ferrer, Juan R. Gonzalez, Laura I. Furlong

Rendered fromgeneral_overview.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-01-11
Started: 2017-03-27

psygenet2r: Case study on GWAS on bipolar disorder

Alba Gutierrez-Sacristan, Carles Hernandez-Ferrer, Juan R. Gonzalez, Laura I. Furlong

Rendered fromcase_study.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-05-22
Started: 2017-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class DataGeNET.Psy	DataGeNET.Psy-class
Enrichment of a user's input (genes) in PsyGeNET's diseases.	enrichedPD
Raw data from 'DataGeNET.Psy' and 'JaccardIndexPsy'.	extract extract,DataGeNET.Psy-method extract,JaccardIndexPsy-method
Method to obtain the sentences that support a gene-disease association from a 'DataGeNET.Psy' object.	extractSentences extractSentences,DataGeNET.Psy-method
Ploting the relation between genes and disease-categories	geneAttrPlot
Query PsyGeNET for given gene(s) and generates an 'DataGeNET.Psy'	getUMLs
Calculation of the Jaccard Index between ideseases	jaccardEstimation
Class JaccardIndexPsy	JaccardIndexPsy-class
Getter from 'DataGeNET.Psy'.	ndisease ndisease,DataGeNET.Psy-method
Getter from 'DataGeNET.Psy'.	ngene ngene,DataGeNET.Psy-method
Query PsyGeNET for given genes and creates a representation in base of their panther-class	pantherGraphic
Plots the content of a 'DataGeNET.Psy' object	DataGeNET.Psy-plot plot,DataGeNET.Psy,ANY-method
Plot the content of a 'JaccardIndexPsy' object.	JaccardIndexPsy-plot plot,JaccardIndexPsy,ANY-method
psygenet2r: Package to query PsyGeNET database and to perform comorbidity studies	psygenet2r-package psygenet2r
Query PsyGeNET for given disease(s) and generates an 'DataGeNET.Psy'	psygenetDisease
Query PsyGeNET for given disease(s) and extract the pmids sentences that report a gene-disease asssociation.	psygenetDiseaseSentences
Query PsyGeNET for given gene(s) and generates an 'DataGeNET.Psy'	psygenetGene
Query PsyGeNET for given gene(s) and extract the pmids sentences that report a gene-disease asssociation.	psygenetGeneSentences
'DataGeNET.Psy' obtained from quering PsyGeNET for gene '4852'.	qr
Enrichment of a user's input (genes) in anatomical terms (TopAnat).	topAnatEnrichment
Vector with gene universe for Jaccard Index	universe