Quick Access to Homology Information

A wrapper for the homologene database by the National Center for Biotechnology Information ('NCBI'). It allows searching for gene homologs across species. Data in this package can be found at < ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build68/>.


Build Statuscodecov

An r package that works as a wrapper to homologene

Available species are

  • Homo sapiens
  • Mus musculus
  • Rattus norvegicus
  • Danio rerio
  • Caenorhabditis elegans
  • Drosophila melanogaster
  • Rhesus macaque

More species can be added on request

Installation

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

Usage

Basic homologene function requires a list of gene symbols or NCBI ids, and an inTax and an outTax. In this example, inTax is the taxon id of mus musculus while outTax is for humans.

homologene(c('Eno2','Mog'), inTax = 10090, outTax = 9606)
## 1  Eno2 ENO2    13807    2026
## 2   Mog  MOG    17441    4340
homologene(c('Eno2','17441'), inTax = 10090, outTax = 9606)
##   10090 9606 10090_ID 9606_ID
## 1  Eno2 ENO2    13807    2026
## 2   Mog  MOG    17441    4340

For mouse and humans two convenience functions exist that removes the need to provide taxonomic identifiers. Note that the column names are not the same as the homologene output.

mouse2human(c('Eno2','Mog'))
##   mouseGene humanGene mouseID humanID
## 1      Eno2      ENO2   13807    2026
## 2       Mog       MOG   17441    4340
human2mouse(c('ENO2','MOG','GZMH'))
##   humanGene mouseGene humanID mouseID
## 1      ENO2      Eno2    2026   13807
## 2       MOG       Mog    4340   17441
## 3      GZMH      Gzmd    2999   14941
## 4      GZMH      Gzme    2999   14942
## 5      GZMH      Gzmg    2999   14944
## 6      GZMH      Gzmf    2999   14943

Mishaps

As of version version 1.1.68, the output now includes NCBI ids. Since it doesn't change any of the existing column names or their order, this shouldn't cause problems in most use cases. If this is an issue for you plase notify me.

If a you can't find a gene you are looking for it may have synonyms. See geneSynonym package to find them. If you have other problems open an issue or send a mail.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("homologene")

1.1.68 by Ogan Mancarci, a year ago


https://github.com/oganm/homologene


Report a bug at https://github.com/oganm/homologene/issues


Browse source code at https://github.com/cran/homologene


Authors: Ogan Mancarci [aut, cre] , Leon French [ctb]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports dplyr, magrittr

Suggests testthat


See at CRAN