Introduction | Installation | Bioconductor install | GitHub install | Input Data | Transductomics data | Pileup files | TrIdentClassifier() | Function components | Contig filtering | Changing pileup windowSize | Pattern-matching | Patterns | Sloping: | Prophage-like: | noPattern: | Highly active/abundant and heterogenously integrated/present Prophage-like elements | NoPattern classifications with high VLP-fraction:whole-community read coverage ratios | Usage | Arguments/Parameters | Output | plotTrIdentResults() | Re-building pattern-matches | Plotting read coverage and associated pattern-matches | specializedTransductionID() | Zoom-in on Prophage-like elements | Identify borders of Prophage-like elements | Search for specialized transduction outside Prophage-like borders | Supplemental information | Usage Note | Acknowledgments | Funding | Session Information
Package: TrIdent 1.4.0
Jessie Maier
TrIdent: TrIdent - Transduction Identification
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.
Authors:
TrIdent_1.4.0.tar.gz
TrIdent_1.4.0.zip(r-4.7-any)TrIdent_1.4.0.zip(r-4.6-any)TrIdent_1.4.0.zip(r-4.5-any)
TrIdent_1.4.0.tgz(r-4.6-any)TrIdent_1.4.0.tgz(r-4.5-any)
TrIdent_1.4.0.tar.gz(r-4.7-any)TrIdent_1.4.0.tar.gz(r-4.6-any)
TrIdent_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TrIdent/json (API)
| # Install 'TrIdent' in R: |
| install.packages('TrIdent', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jlmaier12/trident/issues
Pkgdown/docs site:https://jlmaier12.github.io
On BioConductor:TrIdent-1.5.3(bioc 3.24)TrIdent-1.4.0(bioc 3.23)
coveragemetagenomicspatternlogicclassificationsequencingbacteriophagehorizontal-gene-transferpattern-matchingphagesequencing-coveragetransductiontransductomicsvirus-like-particle
Last updated from:57933f3358 (on RELEASE_3_23). Checks:1 WARNING, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 141 | ||
| linux-devel | OK | 251 | ||
| source / vignettes | OK | 206 | ||
| linux-release | OK | 257 | ||
| macos-release | OK | 119 | ||
| macos-oldrel | OK | 145 | ||
| windows-devel | OK | 90 | ||
| windows-release | OK | 143 | ||
| windows-oldrel | OK | 107 | ||
| wasm-release | OK | 114 |
Exports:plotTrIdentResultsspecializedTransductionIDTrIdentClassifier
Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpatchworkpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadilloRcppParallelrlangrollS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern | plotTrIdentResults |
| Identify potential specialized transduction events on contigs classified as Prophage-like | specializedTransductionID |
| Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern | TrIdentClassifier |