# Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

## Documentation for package ‘DRIMSeq’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-method | MatrixList object
coefficients-method | dmDSfit object
colnames-method | MatrixList object
colnames<--method | MatrixList object
common_precision | dmDSprecision object
common_precision-method | dmDSprecision object
common_precision-method | dmSQTLprecision object
common_precision<- | dmDSprecision object
common_precision<--method | dmDSprecision object
counts-method | dmDSdata object
counts-method | dmSQTLdata object
design-method | dmDSfit object
design-method | dmDSprecision object
design-method | dmDStest object
dim-method | MatrixList object
dmDSdata | Create dmDSdata object
dmDSdata-class | dmDSdata object
dmDSfit-class | dmDSfit object
dmDSprecision-class | dmDSprecision object
dmDStest-class | dmDStest object
dmFilter | Filtering
dmFilter-method | Filtering
dmFit | Fit the Dirichlet-multinomial and/or the beta-binomial full model regression
dmFit-method | Fit the Dirichlet-multinomial and/or the beta-binomial full model regression
dmPrecision | Estimate the precision parameter in the Dirichlet-multinomial model
dmPrecision-method | Estimate the precision parameter in the Dirichlet-multinomial model
dmSQTLdata | Create dmSQTLdata object
dmSQTLdata-class | dmSQTLdata object
dmSQTLfit-class | dmSQTLfit object
dmSQTLprecision-class | dmSQTLprecision object
dmSQTLtest-class | dmSQTLtest object
dmTest | Likelihood ratio test to detect differential transcript/exon usage
dmTest-method | Likelihood ratio test to detect differential transcript/exon usage
dm_plotDataDSInfo | Plot the frequency of present features
dm_plotProportions | Plot feature proportions
elementNROWS-method | MatrixList object
genewise_precision | dmDSprecision object
genewise_precision-method | dmDSprecision object
genewise_precision-method | dmSQTLprecision object
genewise_precision<- | dmDSprecision object
genewise_precision<--method | dmDSprecision object
length-method | MatrixList object
length-method | dmDSdata object
length-method | dmSQTLdata object
MatrixList-class | MatrixList object
mean_expression | dmDSprecision object
mean_expression-method | dmDSprecision object
mean_expression-method | dmSQTLprecision object
names-method | MatrixList object
names-method | dmDSdata object
names-method | dmSQTLdata object
names<--method | MatrixList object
ncol-method | MatrixList object
nrow-method | MatrixList object
plotData | Plot data summary
plotData-method | Plot data summary
plotPrecision | Precision versus mean expression plot
plotPrecision-method | Precision versus mean expression plot
plotProportions | Plot feature proportions
plotProportions-method | Plot feature proportions
plotPValues | Plot p-value distribution
plotPValues-method | Plot p-value distribution
proportions | dmDSfit object
proportions-method | dmDSfit object
results | dmDStest object
results-method | dmDStest object
results-method | dmSQTLtest object
rownames-method | MatrixList object
rownames<--method | MatrixList object
samples | dmDSdata object
samples-method | dmDSdata object
samples-method | dmSQTLdata object
[-method | MatrixList object
[-method | dmDSdata object
[-method | dmSQTLdata object
[[-method | MatrixList object