TrIdent
This is the released version of TrIdent; for the devel version, see TrIdent.
TrIdent - Transduction Identification
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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 |
| 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | TrIdent_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | TrIdent_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | TrIdent_1.4.0.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 |