Package: IVAS 2.27.0

Seonggyun Han

IVAS: Identification of genetic Variants affecting Alternative Splicing

Identification of genetic variants affecting alternative splicing.

Authors:Seonggyun Han, Sangsoo Kim

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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'))

Datasets:

sampleexp - CEU expression data
samplesnp - CEU genotype data
samplesnplocus - Snplocus

On BioConductor:IVAS-2.27.0(bioc 3.21)IVAS-2.26.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology alternativesplicing differentialexpression differentialsplicing geneexpression generegulation regression rnaseq sequencing snp software transcription

4.78 score 1 packages 1 scripts 226 downloads 49 mentions 11 exports 105 dependencies

Last updated 25 days agofrom:19b8da0ae6. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:calSignificant CalSigSNP chrseparate findAlternative findOversnp MsqtlFinder RatioFromFPKM saveBplot Splicingfinder sqtlfinder sQTLsFinder

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot cachem cli codetools colorspace cpp11 crayon curl DBI DelayedArray doParallel dplyr fansi farver fastmap foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 glue gridExtra gtable httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minqa munsell nlme nloptr openssl pillar pkgconfig plogr png purrr R6 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

IVAS : Identification of genetic Variants affecting Alternative Splicing

Rendered fromIVAS.Rnwusingutils::Sweaveon Nov 18 2024.

Last update: 2017-03-09
Started: 2015-01-14

Citation

Development and contributors

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

Usage by other packages (reverse dependencies)