DOI: 10.18129/B9.bioc.EDIRquery  

This is the development version of EDIRquery; for the stable release version, see EDIRquery.

Query the EDIR Database For Specific Gene

Bioconductor version: Development (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 vub.be>

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


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biocViews Genetics, SequenceMatching, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (0.5 years)
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)
Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Source Package EDIRquery_1.3.0.tar.gz
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