1 Introduction | 2 The input data set | 3 The example dataset : data from Geuvadis RNA sequencing project of 1000 Genome samples | 4 Loading data | 5 The ASdb obect | 6 Identification of SQTLs using multiple cores | 7 Visualizing the result | 8 Session Information
Package: IVAS 2.33.0
Seonggyun Han
IVAS: Identification of genetic Variants affecting Alternative Splicing
Identification of genetic variants affecting alternative splicing.
Authors:
IVAS_2.33.0.tar.gz
IVAS_2.33.0.zip(r-4.7)IVAS_2.33.0.zip(r-4.6)IVAS_2.33.0.zip(r-4.5)
IVAS_2.33.0.tgz(r-4.6-any)IVAS_2.33.0.tgz(r-4.5-any)
IVAS_2.33.0.tar.gz(r-4.7-any)IVAS_2.33.0.tar.gz(r-4.6-any)
IVAS_2.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IVAS/json (API)
| # Install 'IVAS' in R: |
| install.packages('IVAS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- sampleexp - CEU expression data
- samplesnp - CEU genotype data
- samplesnplocus - Snplocus
On BioConductor:IVAS-2.33.0(bioc 3.24)IVAS-2.32.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription
Last updated from:f7832a4ccf. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 216 | ||
| linux-devel-x86_64 | WARNING | 489 | ||
| source / vignettes | OK | 308 | ||
| linux-release-x86_64 | WARNING | 429 | ||
| macos-release-arm64 | WARNING | 228 | ||
| macos-oldrel-arm64 | WARNING | 237 | ||
| windows-devel | WARNING | 308 | ||
| windows-release | WARNING | 335 | ||
| windows-oldrel | WARNING | 331 | ||
| wasm-release | OK | 196 |
Exports:calSignificantCalSigSNPchrseparatefindAlternativefindOversnpMsqtlFinderRatioFromFPKMsaveBplotSplicingfindersqtlfindersQTLsFinder
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydoParalleldplyrfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggfortifyggplot2gluegridExtragtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminqanlmenloptropensslpillarpkgconfigpngpurrrR6rbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLXVectoryaml
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 |