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Bioconductor - doubletrouble (development version)

doubletrouble

This is the development version of doubletrouble; for the stable release version, see doubletrouble.

Identification and classification of duplicated genes

Bioconductor version: Development (3.22)

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. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- 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] ORCID: 0000-0002-5314-2964 , Yves Van de Peer [aut] ORCID: 0000-0003-4327-3730

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

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

To install this package, start R (version "4.5") 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")
Identification and classification of duplicated genes HTML R Script Reference Manual PDF NEWS Text Details biocViews Classification, ComparativeGenomics, FunctionalGenomics, Network, Phylogenetics, Software, WholeGenome Version 1.9.0 In Bioconductor since BioC 3.17 (R-4.3) (2 years) License GPL-3 Depends R (>= 4.2.0) Imports syntenet, GenomicRanges, Biostrings, mclust, MSA2dist(>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures System Requirements URL https://github.com/almeidasilvaf/doubletrouble Bug Reports https://support.bioconductor.org/t/doubletrouble See More Package Archives

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

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