Package: IVAS 2.25.0
Seonggyun Han
IVAS: Identification of genetic Variants affecting Alternative Splicing
Identification of genetic variants affecting alternative splicing.
Authors:
IVAS_2.25.0.tar.gz
IVAS_2.25.0.zip(r-4.5)IVAS_2.25.0.zip(r-4.4)IVAS_2.25.0.zip(r-4.3)
IVAS_2.25.0.tgz(r-4.4-any)IVAS_2.25.0.tgz(r-4.3-any)
IVAS_2.25.0.tar.gz(r-4.5-noble)IVAS_2.25.0.tar.gz(r-4.4-noble)
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IVAS.pdf |IVAS.html✨
IVAS/json (API)
NEWS
| # Install 'IVAS' in R: |
| install.packages('IVAS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- sampleexp - CEU expression data
- samplesnp - CEU genotype data
- samplesnplocus - Snplocus
On BioConductor:IVAS-2.25.0(bioc 3.20)IVAS-2.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:6650399d54
Exports:calSignificantCalSigSNPchrseparatefindAlternativefindOversnpMsqtlFinderRatioFromFPKMsaveBplotSplicingfindersqtlfindersQTLsFinder
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbriocachemcallrclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydescdiffobjdigestdoParalleldplyrevaluatefansifarverfastmapforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggfortifyggplot2gluegridExtragtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptropensslpillarpkgbuildpkgconfigpkgloadplogrpngpraiseprocessxpspurrrR6RColorBrewerRcppRcppEigenRCurlrematch2restfulrRhtslibrjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystestthattibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewaldowithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| IVAS : Identification of genomic variants affecting Alternative Splicing | IVAS-package IVAS |
| ASdb s4 class - a container for results from functions of the 'IVAS' package. | ASdb-class |
| Deprecated | calSignificant |
| Calculate significance SNPs | CalSigSNP |
| Separate a TxDb object based on a chromosome. | chrseparate |
| Find alternative exons of a gene. | findAlternative |
| Find SNPs which belong to alternative exons and flanking introns of them. | findOversnp |
| Deprecated functions in package 'IVAS' | IVAS-deprecated |
| Deprecated | MsqtlFinder |
| Estimate relative expression ratio. | RatioFromFPKM |
| CEU expression data | sampleexp |
| CEU genotype data | samplesnp |
| snplocus | samplesnplocus |
| Save boxplots | saveBplot |
| Find alternatively spliced exons | Splicingfinder |
| Deprecated | sqtlfinder |
| Find SQTLs. | sQTLsFinder |