doubletrouble
Identification and classification of duplicated genes
Bioconductor version: 3.23 · Package version: 1.12.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("doubletrouble")Details
| Maintainer | Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com> |
| Author | Fabrício Almeida-Silva [aut, cre] (ORCID: <https://orcid.org/0000-0002-5314-2964>), Yves Van de Peer [aut] (ORCID: <https://orcid.org/0000-0003-4327-3730>) |
| License | GPL-3 |
| URL | https://github.com/almeidasilvaf/doubletrouble |
| Bug Reports | https://support.bioconductor.org/t/doubletrouble |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, ComparativeGenomics, FunctionalGenomics, Network, Phylogenetics, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/doubletrouble/ |
Citation
From within R, enter citation("doubletrouble"):
Fabrício Almeida-Silva, Yves Van de Peer. doubletrouble: Identification and classification of duplicated genes. doi:10.18129/B9.bioc.doubletrouble, R package version 1.12.0, https://bioconductor.org/packages/doubletrouble.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | doubletrouble_1.12.0.tar.gz |
| Windows binary (x86_64) | doubletrouble_1.12.0.zip |
| macOS binary (arm64) | doubletrouble_1.12.0.tgz |
| macOS binary (x86_64) | doubletrouble_1.12.0.tgz |
Dependencies
Depends: R (>= 4.2.0)
Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures
Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo