README.md

In oganm/geneSynonym: Quick Access to Gene Synonym Information

Gene Synonym

An r package that works as a wrapper to synonym information in ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz. Updates semi-regularly since 8th of Match 2017

Available species are

geneSynonym::taxData

##    tax_id                      name_txt
## 1   10090                  Mus musculus
## 2   10116             Rattus norvegicus
## 3   28985          Kluyveromyces lactis
## 4  318829            Magnaporthe oryzae
## 5   33169         Eremothecium gossypii
## 6    3702          Arabidopsis thaliana
## 7    4530                  Oryza sativa
## 8    4896     Schizosaccharomyces pombe
## 9    4932      Saccharomyces cerevisiae
## 10   5141             Neurospora crassa
## 11   6239        Caenorhabditis elegans
## 12   7165             Anopheles gambiae
## 13   7227       Drosophila melanogaster
## 14   7955                   Danio rerio
## 15   8364 Xenopus (Silurana) tropicalis
## 16   9031                 Gallus gallus
## 17   9544                Macaca mulatta
## 18   9598               Pan troglodytes
## 19   9606                  Homo sapiens
## 20   9615        Canis lupus familiaris
## 21   9913                    Bos taurus
## 22    562              Escherichia coli

More species can be added on request

Installation

library(devtools)
install_github('oganm/geneSynonym')

Usage

The output is a nested list since gene synonyms are not nececarilly unique. For instance

mouseSyno('Tex40')

## $Tex40
## $Tex40$`16528`
## [1] "Kcnk4"    "Catsperz" "MLZ-622"  "TRAAK"    "TRAAKt"   "Tex40"   
## 
## $Tex40$`67077`
## [1] "Catsperz"      "1700019N12Rik" "A430107B04Rik" "MLZ-622"      
## [5] "Tex40"

Names of vectors within the list are NCBI ids.

Input is a vector of gene names/NCBI ids and a tax identifier. Alternatively shorthand functions exist for human and mouse.

geneSynonym(c('Eno2','Mog'), tax = 10090)

## $Eno2
## $Eno2$`13807`
## [1] "Eno2"       "D6Ertd375e" "Eno-2"      "NSE"       
## 
## 
## $Mog
## $Mog$`17441`
## [1] "Mog"           "B230317G11Rik"

geneSynonym(c('Eno2','Mog'), tax = 10090)

## $Eno2
## $Eno2$`13807`
## [1] "Eno2"       "D6Ertd375e" "Eno-2"      "NSE"       
## 
## 
## $Mog
## $Mog$`17441`
## [1] "Mog"           "B230317G11Rik"

mouseSyno(c('Eno2',17441))

## $Eno2
## $Eno2$`13807`
## [1] "Eno2"       "D6Ertd375e" "Eno-2"      "NSE"       
## 
## 
## $`17441`
## $`17441`$`17441`
## [1] "Mog"           "B230317G11Rik"

humanSyno('MOG')

## $MOG
## $MOG$`4340`
## [1] "MOG"    "BTN6"   "BTNL11" "MOGIG2" "NRCLP7"

oganm/geneSynonym documentation built on April 29, 2024, 9:54 p.m.