get_mart

Make a connection to the release-matched Ensembl database and saves the object as an RDS file.

module

Inputs

Channel nameDescriptionType
optA map of task-specific variables.map
tagAn identifier to use in the tag directive.string
organismThe organism name (eg. mus musculus) that will be converted to an Ensembl species (eg. mmusculus).string
releaseEnsembl database release version (eg. 101).string

Outputs

Emission nameDescriptionTypeFilename pattern
optA map of task-specific variables.map
taskYAML-formatted file of task parameters and software versions used by the task.filetask.yaml
martRDS object of a biomaRt connection.filemart.rds

Tools

biomart

biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite.

Homepage Documentation Source

r

R is a free software environment for statistical computing and graphics.

Homepage Documentation