Introduction | Structural variation simulation | Simulation of biases towards SV formation mechanisms and repeat regions | Simulation of additional breakpoint mutations | Simulation within a genome subset | Comparing two sets of SVs | Setting structural variation sizes | Runtime | Session Information
Package: RSVSim 1.53.0
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_1.53.0.tar.gz
RSVSim_1.53.0.zip(r-4.7)RSVSim_1.53.0.zip(r-4.6)RSVSim_1.53.0.zip(r-4.5)
RSVSim_1.53.0.tgz(r-4.6-any)RSVSim_1.53.0.tgz(r-4.5-any)
RSVSim_1.53.0.tar.gz(r-4.7-any)RSVSim_1.53.0.tar.gz(r-4.6-any)
RSVSim_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RSVSim/json (API)
| # Install 'RSVSim' in R: |
| install.packages('RSVSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- segDups - Segmental duplications
- weightsMechanisms - Weights for SV formation mechanisms
- weightsRepeats - Weights for repeat region bias
On BioConductor:RSVSim-1.53.0(bioc 3.24)RSVSim-1.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:9485f7ccd9. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 262 | ||
| linux-devel-x86_64 | NOTE | 418 | ||
| source / vignettes | OK | 324 | ||
| linux-release-x86_64 | NOTE | 417 | ||
| macos-release-arm64 | NOTE | 276 | ||
| macos-oldrel-arm64 | NOTE | 255 | ||
| windows-devel | NOTE | 375 | ||
| windows-release | NOTE | 407 | ||
| windows-oldrel | NOTE | 369 | ||
| wasm-release | OK | 204 |
Exports:compareSVestimateSVSizessimulateSV
Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarillocodetoolscpp11crayonDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangeshwriterinterpIRangesjpeglambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatspngpwalignRColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraySummarizedExperimentXVector
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 |
