doubletrouble

DOI: 10.18129/B9.bioc.doubletrouble    

This is the development version of doubletrouble; to use it, please install the devel version of Bioconductor.

Identification and classification of duplicated genes

Bioconductor version: Development (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>

Citation (from within R, enter citation("doubletrouble")):

Installation

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

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

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

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 0.99.2
In Bioconductor since BioC 3.17 (R-4.3)
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_0.99.2.tar.gz
Windows Binary doubletrouble_0.99.2.zip
macOS Binary (x86_64) doubletrouble_0.99.2.tgz
macOS Binary (arm64) doubletrouble_0.99.2.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

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