doubletrouble
This is the development version of doubletrouble; for the stable release version, see doubletrouble.
Identification and classification of duplicated genes
Bioconductor version: Development (3.21)
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: FabrÃcio Almeida-Silva [aut, cre] (ORCID:
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, ComparativeGenomics, FunctionalGenomics, Network, Phylogenetics, Software, WholeGenome |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 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
| Suggests | txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo |
| 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 | doubletrouble_1.7.0.tar.gz |
| Windows Binary (x86_64) | doubletrouble_1.7.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |