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doubletrouble

Identification and classification of duplicated genes


Bioconductor version: Release (3.18)

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] , 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")

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 1.2.5
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports syntenet, GenomicRanges, Biostrings, mclust, MSA2dist(>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures, BiocParallel
System Requirements
URL https://github.com/almeidasilvaf/doubletrouble
Bug Reports https://support.bioconductor.org/t/doubletrouble
See More
Suggests testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo
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Package Archives

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

Source Package doubletrouble_1.2.5.tar.gz
Windows Binary doubletrouble_1.2.5.zip (64-bit only)
macOS Binary (x86_64) doubletrouble_1.2.5.tgz
macOS Binary (arm64) doubletrouble_1.2.5.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 3.18 Source Archive