kissDE-package: Retrieves condition-specific variants in RNA-seq data

In aursiber/kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

Retrieves condition-specific variants in RNA-seq data

Description

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.

Details

Main functions:

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)

kissDE(fileName, conditions, output, counts = 2, pairedEnd = FALSE, order = NULL, exonicReads = TRUE, k2rg = FALSE, keep = c("All"), remove = NULL, pvalue = 1, filterLowCountsVariants = 10, flagLowCountsConditions = 10, technicalReplicates = FALSE, nbCore = 1, adjPvalMax = 1, dPSImin = 0, writePSI = FALSE)

Note

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: Aurélie Siberchicot

aursiber/kissDE documentation built on Jan. 28, 2024, 10:01 a.m.