Package: VaSP 1.19.0
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_1.19.0.tar.gz
VaSP_1.19.0.zip(r-4.5)VaSP_1.19.0.zip(r-4.4)VaSP_1.19.0.zip(r-4.3)
VaSP_1.19.0.tgz(r-4.4-any)VaSP_1.19.0.tgz(r-4.3-any)
VaSP_1.19.0.tar.gz(r-4.5-noble)VaSP_1.19.0.tar.gz(r-4.4-noble)
VaSP_1.19.0.tgz(r-4.4-emscripten)VaSP_1.19.0.tgz(r-4.3-emscripten)
VaSP.pdf |VaSP.html✨
VaSP/json (API)
NEWS
| # 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
- rice.bg - Rice ballgown object
On BioConductor:VaSP-1.19.0(bioc 3.21)VaSP-1.18.0(bioc 3.20)
rnaseqalternativesplicingdifferentialsplicingstatisticalmethodvisualizationpreprocessingclusteringdifferentialexpressionkeggimmunooncology3s-scoresalternative-splicingballgownrna-seqsplicingsqtlstatistics
Last updated 2 months agofrom:f2e104d025. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:BMfindergetDepthgetGeneinfospliceGenespliceGenome
Dependencies:abindannotateAnnotationDbiaskpassballgownBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcliclustercodetoolscpp11crayoncurlDBIDelayedArrayedgeRfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectoryamlzlibbioc
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 |
