Package: syntenyPlotteR 1.0.0
Marta Farre
syntenyPlotteR: Genome Synteny Visualization
Draw syntenic relationships between genome assemblies. There are 3 functions which take a tab delimited file containing alignment data for syntenic blocks between genomes to produce either a linear alignment plot, an evolution highway style plot, or a painted ideogram representing syntenic relationships. There is also a function to convert alignment data in the DESCHRAMBLER/inferCAR format to the required data structure.
Authors:
syntenyPlotteR_1.0.0.tar.gz
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syntenyPlotteR.pdf |syntenyPlotteR.html✨
syntenyPlotteR/json (API)
NEWS
| # Install 'syntenyPlotteR' in R: |
| install.packages('syntenyPlotteR', repos = c('https://farre-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/farre-lab/syntenyplotter/issues
Last updated 12 months agofrom:9623174a88. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-win | OK | Nov 12 2024 |
| R-4.5-linux | OK | Nov 12 2024 |
| R-4.4-win | OK | Nov 12 2024 |
| R-4.4-mac | OK | Nov 12 2024 |
| R-4.3-win | OK | Nov 12 2024 |
| R-4.3-mac | OK | Nov 12 2024 |
Exports:draw.ehdraw.ideogramdraw.linearreformat.syntenyData
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesstringistringrtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Evolution Highway style plot | draw.eh |
| Draw ideograms in chromosome painting style | draw.ideogram |
| Linear synteny plot | draw.linear |
| Reformat synteny data | reformat.syntenyData |