Introduction | Installation | CRAN install | GitHub install | Input data | Pileups | gff TSV | ProActiveDetect() | Function components | Chunking | Filtering | Changing pileup windowSize | Pattern-matching | Elevation pattern: | Gap pattern: | Elevation/Gap pattern: | noPattern: | Calculating elevation ratios | Extracting gene annotations in elevated/gapped regions | Usage | Arguments/parameters | Output | plotProActiveResults() | Re-building pattern-matches | Plotting read coverage and associated pattern-matches | View select metagenome plots | View select genome plots | geneAnnotationSearch() | Search for gene annotations | Plot gene annotation locations | Supplemental information | Funding | Session Information
Package: ProActive 0.1.0.9000
ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Automate the detection of gaps and elevations in mapped sequencing read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes and visualizes read coverage patterns in both genomes and metagenomes. Optionally, users may provide gene annotations associated with their genome or metagenome in the form of a .gff file. In this case, 'ProActive' will generate an additional output table containing the gene annotations found within the detected regions of gapped and elevated read coverage. Additionally, users can search for gene annotations of interest in the output read coverage plots.
Authors:
ProActive_0.1.0.9000.tar.gz
ProActive_0.1.0.9000.zip(r-4.7-any)ProActive_0.1.0.9000.zip(r-4.6-any)ProActive_0.1.0.9000.zip(r-4.5-any)
ProActive_0.1.0.9000.tgz(r-4.6-any)ProActive_0.1.0.9000.tgz(r-4.5-any)
ProActive_0.1.0.9000.tar.gz(r-4.7-any)ProActive_0.1.0.9000.tar.gz(r-4.6-any)
ProActive_0.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ProActive/json (API)
| # Install 'ProActive' in R: |
| install.packages('ProActive', repos = c('https://jlmaier12.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jlmaier12/proactive/issues
Pkgdown/docs site:https://jlmaier12.github.io
bacteriophagemetagenomicsmobile-genetic-elementspattern-matchingprophagesread-mappingsequencing-coveragestructural-variantstransposable-elements
Last updated from:fe522fb8d5. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 186 | ||
| source / vignettes | OK | 221 | ||
| linux-release | OK | 176 | ||
| macos-release | OK | 118 | ||
| macos-oldrel | OK | 158 | ||
| windows-devel | OK | 176 | ||
| windows-release | OK | 124 | ||
| windows-oldrel | OK | 119 | ||
| wasm-release | OK | 107 |
Exports:geneAnnotationSearchplotProActiveResultsProActiveDetect
Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigR6RColorBrewerrlangS7scalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Search for gene annotations on classified contigs/chunks | geneAnnotationSearch |
| Plot results of `ProActive()` pattern-matching | plotProActiveResults |
| Detect elevations and gaps in mapped read coverage patterns. | ProActiveDetect |