DESCRIPTION

Package: TrIdent
Title: 
  Detect Genetic Transduction Events in Metagenomes using Read Coverage 
  Pattern-Matching
Version: 0.0.0.9000
Maintainer: Jessie Maier <jlmaier@ncsu.edu>
Authors@R: 
  c(person(given = "Jessie",
           family = "Maier",
           role = c("aut", "cre", "cph"),
           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: 
  `TrIdent` 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: true
Imports: 
  graphics, 
  utils, 
  stats, 
  dplyr, 
  ggplot2, 
  patchwork, 
  stringr, 
  tidyr, 
  roll
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