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 | geneSearch() | Search for gene annotations | Plot gene annotation locations | Arguments/parameters | Supplemental information | Usage Note | Acknowledgments | Funding | Session Information
Package: TrIdent 1.5.3
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_1.5.3.tar.gz
TrIdent_1.5.3.zip(r-4.7-any)TrIdent_1.5.3.zip(r-4.6-any)TrIdent_1.5.3.zip(r-4.5-any)
TrIdent_1.5.3.tgz(r-4.6-any)TrIdent_1.5.3.tgz(r-4.5-any)
TrIdent_1.5.3.tar.gz(r-4.7-any)TrIdent_1.5.3.tar.gz(r-4.6-any)
TrIdent_1.5.3.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.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:a4ee81929e. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 219 | ||
| linux-devel | OK | 241 | ||
| source / vignettes | OK | 334 | ||
| linux-release | OK | 413 | ||
| macos-release | OK | 167 | ||
| macos-oldrel | OK | 164 | ||
| windows-devel | OK | 135 | ||
| windows-release | OK | 144 | ||
| windows-oldrel | OK | 201 | ||
| wasm-release | OK | 141 |
Exports:geneSearchplotTrIdentResultsspecializedTransductionIDTrIdentClassifier
Dependencies:BiocGenericsclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrnloptrpatchworkpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadilloRcppParallelrlangrollS4VectorsS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Search for gene annotations on positively classified contigs | geneSearch |
| 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 |
