The kissDE package retrieves condition-specific variants in RNA-seq data. Each variation (SNVs, alternative splicing events) is represented as a pair of variants. The quantification of each variant is summarized as a count, in each condition and each replicate where it was measured. The package tests for enrichment of a variant in a condition. Data counts are modelled using either a poisson or a negative binomial. Likelihood ratio tests are then performed using the GLM (Generalized Linear Model) framework.
diffExpressedVariants(countsData, conditions, pvalue = 1, filterLowCountsVariants = 10, flagLowCountsConditions = 10, technicalReplicates = FALSE)
qualityControl(countsData, conditions, storeFigs = FALSE)
kissplice2counts(fileName, counts = 0, pairedEnd = FALSE, order = NULL, exonicReads = TRUE, k2rg = FALSE, keep = c("All"), remove = NULL)
writeOutputKissDE(resDiffExprVariant, output, adjPvalMax = 1, dPSImin = 0, writePSI = FALSE)
Authors of the package: Clara Benoit-Pilven, Camille Marchet, Janice Kielbassa, Lilia Brinza, Audric Cologne and Vincent Lacroix all contributed code and ideas.
Contributors of the package: Franck Picard and Laurent Jacob provided statistical expertise for the models underlying kissDE. Vincent Miele provided expertise for the development of the R package.
Maintainer of the package: Aur<c3><a9>lie Siberchicot
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