Package: RSVSim 1.47.0
Christoph Bartenhagen
RSVSim: RSVSim: an R/Bioconductor package for the simulation of structural variations
RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.
Authors:
RSVSim_1.47.0.tar.gz
RSVSim_1.47.0.zip(r-4.5)RSVSim_1.47.0.zip(r-4.4)RSVSim_1.47.0.zip(r-4.3)
RSVSim_1.47.0.tgz(r-4.4-any)RSVSim_1.47.0.tgz(r-4.3-any)
RSVSim_1.47.0.tar.gz(r-4.5-noble)RSVSim_1.47.0.tar.gz(r-4.4-noble)
RSVSim_1.47.0.tgz(r-4.4-emscripten)RSVSim_1.47.0.tgz(r-4.3-emscripten)
RSVSim.pdf |RSVSim.html✨
RSVSim/json (API)
| # Install 'RSVSim' in R: |
| install.packages('RSVSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- segDups - Segmental duplications
- weightsMechanisms - Weights for SV formation mechanisms
- weightsRepeats - Weights for repeat region bias
On BioConductor:RSVSim-1.47.0(bioc 3.21)RSVSim-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.
Last updated 23 days agofrom:ad6b2ecc1b. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | WARNING | Nov 18 2024 |
| R-4.5-linux | WARNING | Nov 18 2024 |
| R-4.4-win | WARNING | Nov 18 2024 |
| R-4.4-mac | WARNING | Nov 18 2024 |
| R-4.3-win | WARNING | Nov 18 2024 |
| R-4.3-mac | WARNING | Nov 18 2024 |
Exports:compareSVestimateSVSizessimulateSV
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compare the simulation with a set of SVs | compareSV compareSV,character,character-method compareSV,character,data.frame-method compareSV,data.frame,data.frame-method |
| Draw random structural variation sizes from a beta distribution | estimateSVSizes estimateSVSizes,numeric,missing,ANY,ANY,character-method estimateSVSizes,numeric,missing,ANY,ANY,missing-method estimateSVSizes,numeric,numeric,ANY,ANY,missing-method |
| Segmental duplications | segDups |
| Structural Variant Simulation | simulateSV simulateSV,ANY simulateSV,ANY-method |
| Weights for SV formation mechanisms | weightsMechanisms |
| Weights for repeat region bias | weightsRepeats |
