Package: triplex 1.47.0
Jiri Hon
triplex: Search and visualize intramolecular triplex-forming sequences in DNA
This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.
Authors:
triplex_1.47.0.tar.gz
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triplex.pdf |triplex.html✨
triplex/json (API)
NEWS
| # Install 'triplex' in R: |
| install.packages('triplex', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:triplex-1.47.0(bioc 3.21)triplex-1.46.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencematchinggeneregulation
Last updated 23 days agofrom:cc51819b6d. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 14 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 14 2024 |
Exports:inslendlstartlwidthpvaluescoreshowstrandtoStringtriplex.3Dtriplex.alignmenttriplex.diagramtriplex.group.tabletriplex.score.tabletriplex.search
Dependencies:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Triplex search and visualization package | triplex-package triplex |
| Insertions accessor | ins |
| Loop end accessor | lend |
| Loop start accessor | lstart |
| Loop width accessor | lwidth |
| P-value accessor | pvalue |
| Triplex visualization, 3D representation | triplex.3D |
| Triplex alignment | triplex.alignment |
| Triplex visualization, diagram representation | triplex.diagram |
| Get default isogroup tables | triplex.group.table |
| Get default scoring tables | triplex.score.table |
| Search intramolecular triplex-forming sequences in DNA | triplex.search |
| The TriplexViews class | as.character,TriplexViews-method class:TriplexViews ins,TriplexViews-method lend,TriplexViews-method lstart,TriplexViews-method lwidth,TriplexViews-method pvalue,TriplexViews-method score,TriplexViews-method show,TriplexViews-method strand,TriplexViews-method toString,TriplexViews-method TriplexViews TriplexViews-class TriplexViews-constructor type,TriplexViews-method |
