TrIdent

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

TrIdent - Transduction Identification

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DOI: 10.18129/B9.bioc.TrIdent

Bioconductor version: Development (3.23)

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.

Author: Jessie Maier [aut, cre] ORCID iD ORCID: 0009-0001-8575-5386 , Jorden Rabasco [aut, ctb] ORCID iD ORCID: 0000-0002-6971-6678 , Craig Gin [aut] ORCID iD ORCID: 0000-0002-7447-663X , Benjamin Callahan [aut] ORCID iD ORCID: 0000-0002-8752-117X , Manuel Kleiner [aut, ths] ORCID iD ORCID: 0000-0001-6904-0287

Maintainer: Jessie Maier <jlmaier at ncsu.edu>

Citation (from within R, enter citation("TrIdent")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("TrIdent")

For older versions of R, please refer to the appropriate Bioconductor release.