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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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("EDIRquery")

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

Documentation

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

browseVignettes("EDIRquery")
EDIRquery PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Genetics, SequenceMatching, Software
Version 1.3.0
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)
System Requirements
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Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package EDIRquery_1.3.0.tar.gz
Windows Binary EDIRquery_1.3.0.zip
macOS Binary (x86_64) EDIRquery_1.3.0.tgz
macOS Binary (arm64) EDIRquery_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EDIRquery
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EDIRquery
Bioc Package Browser https://code.bioconductor.org/browse/EDIRquery/
Package Short Url https://bioconductor.org/packages/EDIRquery/
Package Downloads Report Download Stats