TrIdent
TrIdent - Transduction Identification
Bioconductor version: 3.23 · Package version: 1.4.0
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 |
| Downloads rank | 142 |
| Source branch | RELEASE_3_23 |
| biocViews | Classification, Coverage, Metagenomics, PatternLogic, Sequencing, Software |