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 (3.21)
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] (ORCID:
Maintainer: Laura D.T. Vo Ngoc <doan.vongoc at vub.be>
citation("EDIRquery")):
Installation
To install this package, start R (version "4.5") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Genetics, SequenceMatching, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 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) |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EDIRquery_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |