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Bioinformatics. 2017 Dec 15;33(24):4004-4006. doi: 10.1093/bioinformatics/btx506.

psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes.

Author information

1
Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM).
2
Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF).
3
ISGlobal, Centre for Research in Environmental Epidemiology (CREAL).
4
CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain.

Abstract

Motivation:

Psychiatric disorders have a great impact on morbidity and mortality. Genotype-phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts.

Results:

We present psygenet2r, an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene's molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders.

Availability and implementation:

The package is implemented in R and is available under MIT license from Bioconductor (http://bioconductor.org/packages/release/bioc/html/psygenet2r.html).

Contact:

juanr.gonzalez@isglobal.org or laura.furlong@upf.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28961763
PMCID:
PMC5860088
DOI:
10.1093/bioinformatics/btx506
[Indexed for MEDLINE]
Free PMC Article

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