EDIRquery

DOI: 10.18129/B9.bioc.EDIRquery  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see EDIRquery.

Query the EDIR Database For Specific Gene

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

PDF	R Script	EDIRquery
PDF		Reference Manual
Text		NEWS

Details

biocViews	Genetics, SequenceMatching, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
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)
LinkingTo
Suggests	knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	EDIRquery_1.0.0.tar.gz
Windows Binary	EDIRquery_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	EDIRquery_1.0.0.tgz
macOS Binary (arm64)	EDIRquery_1.0.0.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