doubletrouble

DOI: 10.18129/B9.bioc.doubletrouble  

Identification and classification of duplicated genes

Bioconductor version: Release (3.17)

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are: i. whole-genome duplication (WGD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). If users want a simpler classification scheme, duplicates can also be classified into WGD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>

Installation

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

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

BiocManager::install("doubletrouble")

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("doubletrouble")

 

HTML	R Script	Identification and classification of duplicated genes
PDF		Reference Manual
Text		NEWS

Details

biocViews	ComparativeGenomics, FunctionalGenomics, Network, Phylogenetics, Software, WholeGenome
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	syntenet, GenomicRanges, Biostrings, mclust, MSA2dist(>= 1.1.5), ggplot2, stats, utils
LinkingTo
Suggests	testthat (>= 3.0.0), knitr, feature, BiocStyle, rmarkdown, covr, sessioninfo
SystemRequirements
Enhances
URL	https://github.com/almeidasilvaf/doubletrouble
BugReports	https://support.bioconductor.org/t/doubletrouble
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	doubletrouble_1.0.0.tar.gz
Windows Binary	doubletrouble_1.0.0.zip
macOS Binary (x86_64)	doubletrouble_1.0.0.tgz
macOS Binary (arm64)	doubletrouble_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/doubletrouble
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/doubletrouble
Bioc Package Browser	https://code.bioconductor.org/browse/doubletrouble/
Package Short Url	https://bioconductor.org/packages/doubletrouble/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive