recipe bioconductor-edirquery

Query the EDIR Database For Specific Gene






EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.

package bioconductor-edirquery

(downloads) docker_bioconductor-edirquery



depends bioconductor-genomicranges:


depends bioconductor-interactionset:


depends r-base:


depends r-readr:


depends r-tibble:


depends r-tictoc:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-edirquery

and update with::

   mamba update bioconductor-edirquery

To create a new environment, run:

mamba create --name myenvname bioconductor-edirquery

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-edirquery/tags`_ for valid values for ``<tag>``)

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