Introduction | Getting Started | Clustering Sequences | Recoding | Clusters | Aligning Clustered Sequences | Alignments By Cluster | Consensus Sequences | De Bruijn Graphs | Appendix
Package: SVAlignR 0.10.5
Kevin R. Coombes
SVAlignR: Recovering Structure of Long Molecules from Structural Variation Data
Implements a method to combine multiple levels of multiple sequence alignment to uncover the structure of complex DNA rearrangements.
Authors:
SVAlignR_0.10.5.tar.gz
SVAlignR_0.10.5.zip(r-4.7-any)SVAlignR_0.10.5.zip(r-4.6-any)
SVAlignR_0.10.5.tar.gz(r-4.7-any)SVAlignR_0.10.5.tar.gz(r-4.6-any)
SVAlignR_0.10.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SVAlignR/json (API)
| # Install 'SVAlignR' in R: |
| install.packages('SVAlignR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- breakpoints - SVAlignR Sample Data
- breakpoints - SVAlignR Sample Data
- longreads - SVAlignR Sample Data
- longreads - SVAlignR Sample Data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:e87320a997. Checks:4 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | ERROR | 219 | ||
| source / vignettes | OK | 236 | ||
| linux-release | ERROR | 239 | ||
| windows-devel | ERROR | 163 | ||
| windows-release | ERROR | 152 | ||
| wasm-release | OK | 150 |
Exports:alignAllClustersalignClusterBreakpointsCiphercountWordsdeBruijndecodeDecompositionGraphencodeexportSGgetEvidenceheatimagemakeSubsMatrixmakeWordsMotifGraphplotplotWordsSequenceClustershowCoverageupdateClusters
Dependencies:apeBiocGenericsBiostringscliclustercolorspacecpp11crayondendextenddigestfarvergenericsggplot2gluegridExtragtableigraphIRangesisobandlabelinglatticelifecyclemagrittrMatrixNameNeedlenlmeoompaBasepkgconfigPolychromeR6RColorBrewerRcpprlangS4VectorsS7scalesscatterplot3dSeqinfostringistringrvctrsviridisviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class '"AlignedCluster"' | alignAllClusters alignCluster AlignedCluster-class image,AlignedCluster-method makeSubsMatrix |
| Class '"Breakpoints"' | Breakpoints Breakpoints-class plot,Breakpoints,missing-method |
| Class '"Cipher"' | Cipher Cipher-class decode encode |
| Support and Evidence for Circular DNA | getEvidence showCoverage |
| Class '"DeBruijn"' | deBruijn DeBruijn-class |
| Class '"SequenceCluster"' | heat plot,SequenceCluster,missing-method SequenceCluster SequenceCluster-class updateClusters |
| Class '"StringGraph"' | DecompositionGraph exportSG MotifGraph plot,StringGraph,ANY-method StringGraph StringGraph-class |
| SVAlignR Sample Data | breakpoints longreads SVAlignR-data |
| Class '"Words"' | countWords makeWords plotWords |