|
addStatusByCutoff()
|
Add status by cutoff |
|
addStatusByRank()
|
Add status by rank |
|
autoEdgerComparison()
|
Automatic edgeR analysis from counts |
|
autoLimmaComparison()
|
Automatic limma analysis |
|
autoPairwiseMatrixTest()
|
Automatic pairwise contrast |
|
contrastsFromDesign()
|
Create contrast matrix from design matrix. |
|
countsToTmm()
|
Normalize counts with TMM |
|
createPairwiseContrasts()
|
Create pariwise contrasts |
|
defaultLogFc()
|
Log 2 of means ratio |
|
designFromSampInfo()
|
Create design matrix from sample metadata |
|
edgerDfFromContrasts()
|
Obtain edgeR results from counts, design and contrasts matrix |
|
fisherExactTest()
|
Measure over-representation using Fisher's Exact Test |
|
gseaFromStats()
|
Gene set enrichment analysis from statistical results |
|
gseaPlot()
|
GSEA plot |
|
heatmapPlot()
|
Heatmap plot |
|
humanHallmarks
|
Human MSigDb hallmarks |
|
limmaDfFromContrasts()
|
Obtain limma results from data, design and contrasts matrix. |
|
messageMappingInfo()
|
Evaluate and print translator df information |
|
nsTestPValue()
|
Not sensitive T test p value |
|
nsTestT()
|
Non sensitive T Test statistic |
|
oraFromStats()
|
Over representation analysis from statistical results |
|
overRepresentationAnalysis()
|
Over-representation analysis |
|
pairwiseMatrixTest()
|
Generic pairwise matrix test |
|
pcaPlot()
|
Simple PCA analysis |
|
sarsCovMat
|
RNA-Seq data of human cell lines infected with sars-cov-2 |
|
sarsCovSampInfo
|
Sample level information for the sars-cov-2 count matrix |
|
singleMatrixTest()
|
Generic single matrix analysis |
|
splitFunMerge()
|
Split, Function and Merge |
|
translateMatrix()
|
Translate matrix rownames |
|
translateMatrixWithDb()
|
Translate matrix rownames using annotation package |
|
translateSE()
|
Translate SummarizedExperiment |
|
translateSEWithDb()
|
Translate SummarizedExperiment with annotation package |
|
validateMatrix()
|
Validate matrix |
|
validateSampInfo()
|
Validate sample information |
|
validateTranslatorDf()
|
Validate translator data frame |
|
violinPlot()
|
Violin plot |
|
volcanoPlot()
|
Simple Volcano Plot |