Package: TrIdent
Type: Package
BiocType: Software
Title: TrIdent - Transduction Identification
Version: 1.1.4
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 = "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
biocViews: Coverage, Metagenomics, PatternLogic, Classification,
        Sequencing
RoxygenNote: 7.3.2
URL: https://github.com/jlmaier12/TrIdent,
        https://jlmaier12.github.io/TrIdent/
BugReports: https://github.com/jlmaier12/TrIdent/issues
Suggests: BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 4.2.0)
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/TrIdent
git_branch: devel
git_last_commit: 55904e9
git_last_commit_date: 2025-06-11
Repository: Bioconductor 3.22
Date/Publication: 2025-06-11
NeedsCompilation: no
Packaged: 2025-06-12 02:35:00 UTC; biocbuild
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>)
Maintainer: Jessie Maier <jlmaier@ncsu.edu>
Built: R 4.5.0; ; 2025-06-12 14:04:05 UTC; windows
