1. Introduction | 2. Citation | 3. Installation | 4. Data input | 5. Quick start | 6. Functions | 6.1 getDepth | 6.2 getGeneinfo | 6.3 spliceGene | 6.4 spliceGenome | 6.5 BMfinder | 6.6 splicePlot | 7. Session Information
Package: VaSP 1.25.0
Huihui Yu
VaSP: Quantification and Visualization of Variations of Splicing in Population
Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)
Authors:
VaSP_1.25.0.tar.gz
VaSP_1.25.0.zip(r-4.7)VaSP_1.25.0.zip(r-4.6)VaSP_1.25.0.zip(r-4.5)
VaSP_1.25.0.tgz(r-4.6-any)VaSP_1.25.0.tgz(r-4.5-any)
VaSP_1.25.0.tar.gz(r-4.7-any)VaSP_1.25.0.tar.gz(r-4.6-any)
VaSP_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VaSP/json (API)
| # Install 'VaSP' in R: |
| install.packages('VaSP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yuhuihui2011/vasp/issues
Datasets:
- rice.bg - Rice ballgown object
On BioConductor:VaSP-1.23.0(bioc 3.23)VaSP-1.22.0(bioc 3.22)
rnaseqalternativesplicingdifferentialsplicingstatisticalmethodvisualizationpreprocessingclusteringdifferentialexpressionkeggimmunooncology3s-scoresalternative-splicingballgownrna-seqsplicingsqtlstatistics
Last updated from:e2d52d774b. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
The latest version of this package failed to build. Look at thebuild logs for more information.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 192 | ||
| linux-devel-x86_64 | NOTE | 426 | ||
| source / vignettes | OK | 307 | ||
| linux-release-x86_64 | NOTE | 358 | ||
| macos-release-arm64 | NOTE | 329 | ||
| macos-oldrel-arm64 | NOTE | 191 | ||
| windows-devel | NOTE | 445 | ||
| windows-release | NOTE | 263 | ||
| windows-oldrel | NOTE | 276 | ||
| wasm-release | OK | 173 |
Exports:BMfindergetDepthgetGeneinfospliceGenespliceGenome
Dependencies:abindannotateAnnotationDbiaskpassballgownBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarillocliclustercodetoolscpp11crayoncurlDBIDelayedArrayedgeRfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpkgconfigpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystatmodSummarizedExperimentsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Discover bimodal distrubition features | BMfinder |
| Get Read Depth | getDepth |
| Get Gene Informaton from a ballgown object | getGeneinfo |
| Rice ballgown object | rice.bg |
| Calculate Splicing Scores for One Gene | spliceGene |
| Calculate Genome-wide Splicing Scores | spliceGenome |
