Package: TrIdent
Type: Package
BiocType: Software
Title: TrIdent - Transduction Identification
Version: 1.5.1
Authors@R: 
  c(person(given = "Jessie",
           family = "Maier",
           role = c("aut", "cre"),
           email = "jlmaier@ncsu.edu",
           comment = c(ORCID = "0009-0001-8575-5386")),
    person(given = "Yixuan",
           family = "Yang",
           role = c("aut", "ctb"),
           comment = c(ORCID = "0009-0003-5064-6512")),
    person(given = "Jorden",
           family = "Rabasco",
           role = c("aut", "ctb"),
           comment = c(ORCID = "0000-0002-6971-6678")),
    person(given="Craig", 
           family="Gin",
           role=c("aut"),
           comment=c(ORCID= "0000-0002-7447-663X")),
    person(given="Benjamin",
           family="Callahan",
           role=c("aut"),
           comment=c(ORCID= "0000-0002-8752-117X")),
    person(given="Manuel",
           family="Kleiner",
           role=c("aut","ths"),
           comment=c(ORCID= "0000-0001-6904-0287")))
Description: 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.
License: GPL-2
Encoding: UTF-8
LazyData: false
Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr,
        tidyr, roll, nloptr
biocViews: Coverage, Metagenomics, PatternLogic, Classification,
        Sequencing
URL: https://github.com/jlmaier12/TrIdent,
        https://jlmaier12.github.io/TrIdent/
BugReports: https://github.com/jlmaier12/TrIdent/issues
Suggests: BiocStyle, knitr, rmarkdown, kableExtra
VignetteBuilder: knitr
Depends: R (>= 4.2.0)
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-30 23:44:50 UTC
RemoteUrl: https://github.com/bioc/TrIdent
RemoteRef: HEAD
RemoteSha: 8c11250f412b136dc2916ac09b5805625a8d76f2
NeedsCompilation: no
Packaged: 2026-07-04 06:01:29 UTC; root
Author: Jessie Maier [aut, cre] (ORCID:
    <https://orcid.org/0009-0001-8575-5386>),
  Yixuan Yang [aut, ctb] (ORCID: <https://orcid.org/0009-0003-5064-6512>),
  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>)
Maintainer: Jessie Maier <jlmaier@ncsu.edu>