Differential transcript usage and tuQTL analyses with
Dirichlet-multinomial model in RNA-seq
c(person(given = "Malgorzata", family = "Nowicka", 
    role = c("aut", "cre"),
    email = "gosia.nowicka.uzh@gmail.com"))
The package provides two frameworks. One for the differential
    transcript usage analysis between different conditions and one for the tuQTL analysis.
    Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also
    makes available functions for visualization and exploration of the data and
    results.
ImmunoOncology, SNP, AlternativeSplicing,
DifferentialSplicing, Genetics, RNASeq, Sequencing,
WorkflowStep, MultipleComparison, GeneExpression,
DifferentialExpression
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
'DRIMSeq.R' 'class_show_utils.R' 'class_MatrixList.R'
'class_dmDSdata.R' 'class_dmDSprecision.R' 'class_dmDSfit.R'
'class_dmDStest.R' 'class_dmSQTLdata.R'
'class_dmSQTLprecision.R' 'class_dmSQTLfit.R'
'class_dmSQTLtest.R' 'dmDS_CRadjustment.R'
'dmDS_estimateCommonPrecision.R'
'dmDS_estimateTagwisePrecision.R' 'dmDS_filter.R' 'dmDS_fit.R'
'dmDS_profileLik.R' 'dmSQTL_CRadjustment.R'
'dmSQTL_estimateCommonPrecision.R'
'dmSQTL_estimateTagwisePrecision.R' 'dmSQTL_filter.R'
'dmSQTL_fit.R' 'dmSQTL_permutations.R' 'dmSQTL_profileLik.R'
'dm_CRadjustmentManyGroups.R' 'dm_CRadjustmentOneGroup.R'
'dm_CRadjustmentRegression.R' 'dm_LRT.R' 'dm_core_Hessian.R'
'dm_core_colorb.R' 'dm_core_deviance.R' 'dm_core_lik.R'
'dm_core_score.R' 'dm_estimateMeanExpression.R'
'dm_fitManyGroups.R' 'dm_fitOneGroup.R' 'dm_fitRegression.R'
'dm_plotData.R' 'dm_plotPrecision.R' 'dm_plotProportions.R'
'dm_plotPvalues.R' 'dm_profileLikModeration.R'