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Query the EDIR Database For Specific Gene

Bioconductor version: Release (3.19)

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.

Author: Laura D.T. Vo Ngoc [aut, cre]

Maintainer: Laura D.T. Vo Ngoc <doan.vongoc at>

Citation (from within R, enter citation("EDIRquery")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

EDIRquery PDF R Script
Reference Manual PDF


biocViews Genetics, SequenceMatching, Software
Version 1.4.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet(>= 1.22.0), GenomicRanges(>= 1.46.1)
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Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package EDIRquery_1.4.0.tar.gz
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macOS Binary (x86_64) EDIRquery_1.4.0.tgz
macOS Binary (arm64) EDIRquery_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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