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

Global functions
$,MatrixList-method Man page
MatrixList Source code
MatrixList-class Man page
[,MatrixList,ANY-method Man page
[,MatrixList-method Man page
[,dmDSdata,ANY-method Man page
[,dmDSdata-method Man page
[,dmSQTLdata,ANY-method Man page
[,dmSQTLdata-method Man page
[[,MatrixList-method Man page
addUniform Source code
bbDS_fit Source code
bbDS_fitManyGroups_gene Source code
bbDS_fitRegression_gene Source code
bb_fitManyGroups Source code
bb_fitOneGroup Source code
bb_fitRegression Source code
bb_likG Source code
bb_lik_regG_prop Source code
blocks_per_gene Source code
coefficients,dmDSfit-method Man page
colnames,MatrixList-method Man page
colnames<-,MatrixList-method Man page
colorb Source code
common_precision Man page
common_precision,dmDSprecision-method Man page
common_precision,dmSQTLprecision-method Man page
common_precision<- Man page
common_precision<-,dmDSprecision-method Man page
counts,dmDSdata-method Man page
counts,dmSQTLdata-method Man page
design,dmDSfit-method Man page
design,dmDSprecision-method Man page
design,dmDStest-method Man page
dim,MatrixList-method Man page
dmDS_CRadjustment Source code
dmDS_CRadjustmentManyGroups_gene Source code
dmDS_CRadjustmentRegression_gene Source code
dmDS_estimateCommonPrecision Source code
dmDS_estimateTagwisePrecision Source code
dmDS_filter Source code
dmDS_fit Source code
dmDS_fitManyGroups_gene Source code
dmDS_fitRegression_gene Source code
dmDS_profileLik Source code
dmDS_profileLikCommon Source code
dmDSdata Man page Source code
dmDSdata-class Man page
dmDSfit-class Man page
dmDSprecision-class Man page
dmDStest-class Man page
dmFilter Man page
dmFilter,dmDSdata-method Man page
dmFilter,dmSQTLdata-method Man page
dmFit Man page
dmFit,dmDSprecision-method Man page
dmFit,dmSQTLprecision-method Man page
dmPrecision Man page
dmPrecision,dmDSdata-method Man page
dmPrecision,dmSQTLdata-method Man page
dmSQTL_CRadjustment Source code
dmSQTL_CRadjustmentManyGroups_gene Source code
dmSQTL_CRadjustmentRegression_gene Source code
dmSQTL_estimateCommonPrecision Source code
dmSQTL_estimateTagwisePrecision Source code
dmSQTL_filter Source code
dmSQTL_filter_genotypes_per_gene Source code
dmSQTL_fit Source code
dmSQTL_fitManyGroups_gene Source code
dmSQTL_fitRegression_gene Source code
dmSQTL_permutations_all_genes Source code
dmSQTL_permutations_per_gene Source code
dmSQTL_profileLik Source code
dmSQTL_profileLikCommon Source code
dmSQTLdata Man page Source code
dmSQTLdata-class Man page
dmSQTLfit-class Man page
dmSQTLprecision-class Man page
dmSQTLtest-class Man page
dmTest Man page
dmTest,dmDSfit-method Man page
dmTest,dmSQTLfit-method Man page
dm_CRadjustmentManyGroups Source code
dm_CRadjustmentOneGroup Source code
dm_CRadjustmentRegression Source code
dm_Hessian Source code
dm_HessianG Source code
dm_Hessian_regG Source code
dm_Hessian_regG_prop Source code
dm_LRT Source code
dm_devG Source code
dm_estimateMeanExpression Source code
dm_fitManyGroups Source code
dm_fitOneGroup Source code
dm_fitRegression Source code
dm_lik Source code
dm_likG Source code
dm_likG_neg Source code
dm_lik_regG Source code
dm_lik_regG_neg Source code
dm_lik_regG_prop Source code
dm_movingAverageByCol Source code
dm_plotDataBlocks Source code
dm_plotDataDSInfo Man page Source code
dm_plotDataFeatures Source code
dm_plotDataSnps Source code
dm_plotPValues Source code
dm_plotPrecision Source code
dm_plotProportions Man page Source code
dm_plotProportions_barplot Source code
dm_plotProportions_boxplot1 Source code
dm_plotProportions_boxplot2 Source code
dm_plotProportions_lineplot Source code
dm_plotProportions_ribbonplot Source code
dm_profileLikModeration Source code
dm_score Source code
dm_scoreG Source code
dm_scoreG_neg Source code
dm_score_regG Source code
dm_score_regG_neg Source code
elementNROWS,MatrixList-method Man page
genewise_precision Man page
genewise_precision,dmDSprecision-method Man page
genewise_precision,dmSQTLprecision-method Man page
genewise_precision<- Man page
genewise_precision<-,dmDSprecision-method Man page
length,MatrixList-method Man page
length,dmDSdata-method Man page
length,dmSQTLdata-method Man page
m_Hessian_regG Source code
mean_expression Man page
mean_expression,dmDSprecision-method Man page
mean_expression,dmSQTLprecision-method Man page
names,MatrixList-method Man page
names,dmDSdata-method Man page
names,dmSQTLdata-method Man page
names<-,MatrixList-method Man page
ncol,MatrixList-method Man page
nrow,MatrixList-method Man page
plotData Man page
plotData,dmDSdata-method Man page
plotData,dmSQTLdata-method Man page
plotPValues Man page
plotPValues,dmDStest-method Man page
plotPValues,dmSQTLtest-method Man page
plotPrecision Man page
plotPrecision,dmDSprecision-method Man page
plotPrecision,dmSQTLprecision-method Man page
plotProportions Man page
plotProportions,dmDSfit-method Man page
plotProportions,dmSQTLfit-method Man page
proportions Man page
proportions,dmDSfit-method Man page
results Man page
results,dmDStest-method Man page
results,dmSQTLtest-method Man page
rownames,MatrixList-method Man page
rownames<-,MatrixList-method Man page
samples Man page
samples,dmDSdata-method Man page
samples,dmSQTLdata-method Man page
show_MatrixList_list Source code
show_matrix Source code
show_numeric Source code
show_numeric_list Source code
DRIMSeq documentation built on Jan. 5, 2019, 6:39 p.m.