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

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Documentation for package ‘DRIMSeq’ version 1.16.0

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$-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