GitHub - oganm/geneSynonym: Quick access to gene synonyms (original) (raw)
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
## 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
## $Tex40
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>T</mi><mi>e</mi><mi>x</mi><mn>40</mn></mrow><annotation encoding="application/x-tex">Tex40</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6833em;"></span><span class="mord mathnormal" style="margin-right:0.13889em;">T</span><span class="mord mathnormal">e</span><span class="mord mathnormal">x</span><span class="mord">40</span></span></span></span>`16528`
## [1] "Kcnk4" "Catsperz" "MLZ-622" "TRAAK" "TRAAKt" "Tex40"
##
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>T</mi><mi>e</mi><mi>x</mi><mn>40</mn></mrow><annotation encoding="application/x-tex">Tex40</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6833em;"></span><span class="mord mathnormal" style="margin-right:0.13889em;">T</span><span class="mord mathnormal">e</span><span class="mord mathnormal">x</span><span class="mord">40</span></span></span></span>`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
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>E</mi><mi>n</mi><mi>o</mi><mn>2</mn></mrow><annotation encoding="application/x-tex">Eno2</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6833em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mord mathnormal">n</span><span class="mord mathnormal">o</span><span class="mord">2</span></span></span></span>`13807`
## [1] "Eno2" "D6Ertd375e" "Eno-2" "NSE"
##
##
## $Mog
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>M</mi><mi>o</mi><mi>g</mi></mrow><annotation encoding="application/x-tex">Mog</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8778em;vertical-align:-0.1944em;"></span><span class="mord mathnormal" style="margin-right:0.10903em;">M</span><span class="mord mathnormal">o</span><span class="mord mathnormal" style="margin-right:0.03588em;">g</span></span></span></span>`17441`
## [1] "Mog" "B230317G11Rik"
geneSynonym(c('Eno2','Mog'), tax = 10090)
## $Eno2
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>E</mi><mi>n</mi><mi>o</mi><mn>2</mn></mrow><annotation encoding="application/x-tex">Eno2</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6833em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mord mathnormal">n</span><span class="mord mathnormal">o</span><span class="mord">2</span></span></span></span>`13807`
## [1] "Eno2" "D6Ertd375e" "Eno-2" "NSE"
##
##
## $Mog
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>M</mi><mi>o</mi><mi>g</mi></mrow><annotation encoding="application/x-tex">Mog</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8778em;vertical-align:-0.1944em;"></span><span class="mord mathnormal" style="margin-right:0.10903em;">M</span><span class="mord mathnormal">o</span><span class="mord mathnormal" style="margin-right:0.03588em;">g</span></span></span></span>`17441`
## [1] "Mog" "B230317G11Rik"
mouseSyno(c('Eno2',17441))
## $Eno2
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>E</mi><mi>n</mi><mi>o</mi><mn>2</mn></mrow><annotation encoding="application/x-tex">Eno2</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6833em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mord mathnormal">n</span><span class="mord mathnormal">o</span><span class="mord">2</span></span></span></span>`13807`
## [1] "Eno2" "D6Ertd375e" "Eno-2" "NSE"
##
##
## $`17441`
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi mathvariant="normal">‘</mi><mn>17441</mn><mi mathvariant="normal">‘</mi></mrow><annotation encoding="application/x-tex">`17441`</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6944em;"></span><span class="mord">‘17441‘</span></span></span></span>`17441`
## [1] "Mog" "B230317G11Rik"
## $MOG
## <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>M</mi><mi>O</mi><mi>G</mi></mrow><annotation encoding="application/x-tex">MOG</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.6833em;"></span><span class="mord mathnormal">MOG</span></span></span></span>`4340`
## [1] "MOG" "BTN6" "BTNL11" "MOGIG2" "NRCLP7"