bihealth / orthomapper

Offline ortholog mapping

Orthomaper

Orthomapper uses an NCBI database of orthologs to retrieve orthologs between two bilaterian taxons.

Installation

git clone [e-mail]:january.weiner/orthomapper.git
R CMD INSTALL orthomapper

Note: the package is quite large (~130 MB), as it contains the orthology DB.

Example

Here are some examples of things you can do with orthomapper:

## get all orthologs between mouse and rat
mouserat <- orthologs(10090, 10116)

## get the SYMBOL for gene 52024, infer taxon automatically
entrez_annotate(52024)

## get more information on the gene ID 52024
entrez_annotate(52024, taxon=10090, c("SYMBOL", "GENENAME"))

## get all orthologs of the gene ID 52024
ankrd22.o <- orthologs_all(52024)

## map a list of genes to orthologs from another taxon
orthomap(c(229898, 52024), 10090, 9606)

## find a gene symbol by similarity search
similar_symbol("GBP5", 10090)

## get all the species in the databse
species_info()

## what is taxon 9606?
species_info(9606)

## what is the taxon ID of the mouse?
species_search("mouse")

For more information, refer to the package vignette:

vignette("orthomapper")