TrIdent

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

TrIdent - Transduction Identification

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: 0009-0001-8575-5386 , Jorden Rabasco [aut, ctb] ORCID: 0000-0002-6971-6678 , Craig Gin [aut] ORCID: 0000-0002-7447-663X , Benjamin Callahan [aut] ORCID: 0000-0002-8752-117X , Manuel Kleiner [aut, ths] 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TrIdent")

TrIdent	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Coverage, Metagenomics, PatternLogic, Sequencing, Software
Version	1.3.2
In Bioconductor since	BioC 3.21 (R-4.5) (0.5 years)
License	GPL-2
Depends	R (>= 4.2.0)
Imports	graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll
System Requirements
URL	https://github.com/jlmaier12/TrIdent https://jlmaier12.github.io/TrIdent/
Bug Reports	https://github.com/jlmaier12/TrIdent/issues

Suggests	BiocStyle, knitr, rmarkdown, kableExtra
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	TrIdent_1.3.2.tar.gz
Windows Binary (x86_64)	TrIdent_1.3.0.zip
macOS Binary (x86_64)	TrIdent_1.3.0.tgz
macOS Binary (arm64)	TrIdent_1.3.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TrIdent
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TrIdent
Bioc Package Browser	https://code.bioconductor.org/browse/TrIdent/
Package Short Url	https://bioconductor.org/packages/TrIdent/
Package Downloads Report	Download Stats