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 (3.24)
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("EDIRquery")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | EDIRquery_1.13.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | EDIRquery_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | EDIRquery_1.13.0.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 |