IVAS-package
(Package: IVAS) :
IVAS : Identification of genomic variants affecting Alternative Splicing
The tool is to detect genomic variants affecting the alternative splicing using genotypic and gene expression data(RNA-seq).
● Data Source:
BioConductor
● Keywords: package
● Alias: IVAS, IVAS-package
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This function enables one to analyze multiple genes using multi-thread version of the foreach function and joins output results from sqtlfinder function. Moreover, it calculates the FDR using P-values of the matrix result data.
● Data Source:
BioConductor
● Keywords:
● Alias: MsqtlFinder
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calculates P.values for association between expressions and genotypes by using the linear regression model and/or generalized linear mixed model.
● Data Source:
BioConductor
● Keywords:
● Alias: calSignificant
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With the isActiveSeq method in GenomicFeatures package, this function filters the transcriptDb object in the GenomicFeatures package based on a single chromosome.
● Data Source:
BioConductor
● Keywords:
● Alias: chrseparate
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Search alternative exons among transcript isoforms from a single gene.
● Data Source:
BioConductor
● Keywords:
● Alias: findAlternative
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Find SNPs which belong to alternative exons and flanking introns of them.
● Data Source:
BioConductor
● Keywords:
● Alias: findOversnp
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Save boxplots
● Data Source:
BioConductor
● Keywords:
● Alias: saveBplot
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Find significant SNPs using the calSignificant function.
● Data Source:
BioConductor
● Keywords:
● Alias: sqtlfinder
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providing 
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