TrIdent
TrIdent - Transduction Identification
Bioconductor version: 3.23 · Package version: 1.4.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The `TrIdent` R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TrIdent")Details
| Maintainer | Jessie Maier <jlmaier@ncsu.edu> |
| Author | Jessie Maier [aut, cre] (ORCID: <https://orcid.org/0009-0001-8575-5386>), Jorden Rabasco [aut, ctb] (ORCID: <https://orcid.org/0000-0002-6971-6678>), Craig Gin [aut] (ORCID: <https://orcid.org/0000-0002-7447-663X>), Benjamin Callahan [aut] (ORCID: <https://orcid.org/0000-0002-8752-117X>), Manuel Kleiner [aut, ths] (ORCID: <https://orcid.org/0000-0001-6904-0287>) |
| License | GPL-2 |
| URL | https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/ |
| Bug Reports | https://github.com/jlmaier12/TrIdent/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, Coverage, Metagenomics, PatternLogic, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/TrIdent/ |
Citation
From within R, enter citation("TrIdent"):
Jessie Maier, Jorden Rabasco, Craig Gin, Benjamin Callahan, Manuel Kleiner. TrIdent: TrIdent - Transduction Identification. doi:10.18129/B9.bioc.TrIdent, R package version 1.4.0, https://bioconductor.org/packages/TrIdent.
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 | TrIdent_1.4.0.tar.gz |
| Windows binary (x86_64) | TrIdent_1.4.0.zip |
| macOS binary (arm64) | TrIdent_1.4.0.tgz |
| macOS binary (x86_64) | TrIdent_1.4.0.tgz |