TrIdent
This is the released version of TrIdent; for the devel version, see TrIdent.
TrIdent - Transduction Identification
Bioconductor version: Release (3.21)
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]
, Jorden Rabasco [aut, ctb]
, Craig Gin [aut]
, Benjamin Callahan [aut]
, Manuel Kleiner [aut, ths]
Maintainer: Jessie Maier <jlmaier at ncsu.edu>
citation("TrIdent")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Coverage, Metagenomics, PatternLogic, Sequencing, Software |
| Version | 1.0.0 |
| 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | TrIdent_1.0.0.zip |
| macOS Binary (x86_64) | TrIdent_1.0.0.tgz |
| macOS Binary (arm64) | TrIdent_1.0.0.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 |