addPoints	addPoints
addTextLabels	addTextLabels
adjustLayout	adjustLayout
annotatedHeatmap	annotatedHeatmap
anova_pca_metadata	anova_pca_metadata
assaydatatable	assaydatatable
assaydatatableInput	assaydatatableInput
assaydatatableOutput	assaydatatableOutput
barcode_plot	barcode_plot
barplot	barplot
barplotInput	barplotInput
barplotOutput	barplotOutput
bootstrapMedian	bootstrapMedian
boxplot	boxplot
boxplotInput	boxplotInput
boxplotOutput	boxplotOutput
calculateDendrogram	calculateDendrogram
calculateDist	calculateDist
calculatePCAFractionExplained	calculatePCAFractionExplained
cardinalNumericField	cardinalNumericField
checkListIsSubset	checkListIsSubset
chipseq	chipseq
chipseqInput	chipseqInput
chooseGroupingVariables	chooseGroupingVariables
clustering	clustering
clusteringDendrogram	clusteringDendrogram
clusteringInput	clusteringInput
clusteringOutput	clusteringOutput
colGeomMeans	colGeomMeans
colMedians	colMedians
colormaker	colormaker
colormakerInput	colormakerInput
compilePCAData	compilePCAData
compile_contrast_data	compile_contrast_data
cond_log2_transform_assays	cond_log2_transform_assays
cond_log2_transform_matrix	cond_log2_transform_matrix
contrasts	contrasts
contrastsInput	contrastsInput
contrastsOutput	contrastsOutput
convertIds	convertIds
dendro	dendro
dendroInput	dendroInput
dendroOutput	dendroOutput
dexseqplot	dexseqplot
dexseqplotInput	dexseqplotInput
dexseqplotOutput	dexseqplotOutput
dexseqtable	dexseqtable
dexseqtableInput	dexseqtableInput
dexseqtableInputFields	dexseqtableInputFields
dexseqtableOutput	dexseqtableOutput
differentialtable	differentialtable
differentialtableInput	differentialtableInput
differentialtableOutput	differentialtableOutput
drawLines	drawLines
eselistfromConfig	eselistfromConfig
eselistFromYAML	eselistFromYAML
evaluateCardinalFilter	evaluateCardinalFilter
experimenttable	experimenttable
experimenttableInput	experimenttableInput
experimenttableOutput	experimenttableOutput
ExploratorySummarizedExperiment	ExploratorySummarizedExperiment
ExploratorySummarizedExperiment-class	ExploratorySummarizedExperiment-class
ExploratorySummarizedExperimentList	ExploratorySummarizedExperimentList
ExploratorySummarizedExperimentList-class	ExploratorySummarizedExperimentList-class
fieldSets	fieldSets
foldChange	foldChange
foldchangeplot	foldchangeplot
foldchangeplotInput	foldchangeplotInput
foldchangeplotOutput	foldchangeplotOutput
gene	gene
geneBarplot	geneBarplot
geneInput	geneInput
geneModelPlot	geneModelPlot
geneOutput	geneOutput
geneselect	geneselect
geneselectInput	geneselectInput
genesetanalysistable	genesetanalysistable
genesetanalysistableInput	genesetanalysistableInput
genesetanalysistableOutput	genesetanalysistableOutput
genesetbarcodeplot	genesetbarcodeplot
genesetbarcodeplotInput	genesetbarcodeplotInput
genesetbarcodeplotOutput	genesetbarcodeplotOutput
genesetselect	genesetselect
genesetselectInput	genesetselectInput
geom_mean	geom_mean
getExtension	getExtension
getSeparator	getSeparator
ggplotify	ggplotify
ggplot_boxplot	ggplot_boxplot
ggplot_densityplot	ggplot_densityplot
groupby	groupby
groupbyInput	groupbyInput
heatmap	heatmap
heatmapInput	heatmapInput
heatmapOutput	heatmapOutput
hiddenInput	hiddenInput
idToLabel	idToLabel
illuminaarray	illuminaarray
illuminaarrayInput	illuminaarrayInput
illuminaarrayqc	illuminaarrayqc
illuminaarrayqcInput	illuminaarrayqcInput
illuminaarrayqcOutput	illuminaarrayqcOutput
inlineField	inlineField
interactiveHeatmap	interactiveHeatmap
interleaveColumns	interleaveColumns
is_valid_positive_integer_vector	is_valid_positive_integer_vector
labelMatrix	labelMatrix
labelselectfield	labelselectfield
labelselectfieldInput	labelselectfieldInput
linkMatrix	linkMatrix
madScore	madScore
makeAnnotationColors	makeAnnotationColors
makeColorScale	makeColorScale
makeContrastControl	makeContrastControl
makeContrastFilterSet	makeContrastFilterSet
makePackageCitation	makePackageCitation
maplot	maplot
maplotInput	maplotInput
maplotOutput	maplotOutput
modalInput	modalInput
modalOutput	modalOutput
na.replace	na.replace
nlines	nlines
pca	pca
pcaInput	pcaInput
pcaOutput	pcaOutput
plotdownload	plotdownload
plotdownloadInput	plotdownloadInput
plotly_boxplot	plotly_boxplot
plotly_densityplot	plotly_densityplot
plotly_quartiles	plotly_quartiles
plotly_scatterplot	plotly_scatterplot
prepareApp	prepareApp
prettifyGeneSetName	prettifyGeneSetName
prettifyVariablename	prettifyVariablename
pushToList	pushToList
readreports	readreports
readreportsInput	readreportsInput
readreportsOutput	readreportsOutput
read_contrasts	read_contrasts
read_differential	read_differential
read_matrix	read_matrix
read_metadata	read_metadata
rnaseq	rnaseq
rnaseqInput	rnaseqInput
rowmetatable	rowmetatable
rowmetatableInput	rowmetatableInput
rowmetatableOutput	rowmetatableOutput
runPCA	runPCA
sampleselect	sampleselect
sampleselectInput	sampleselectInput
scatterplot	scatterplot
scatterplotcontrols	scatterplotcontrols
scatterplotcontrolsInput	scatterplotcontrolsInput
scatterplotInput	scatterplotInput
scatterplotOutput	scatterplotOutput
selectmatrix	selectmatrix
selectmatrixInput	selectmatrixInput
selectVariableGenes	selectVariableGenes
shinyngs	shinyngs
simpleApp	simpleApp
simpleSplit	simpleSplit
simpletable	simpletable
simpletableInput	simpletableInput
simpletableOutput	simpletableOutput
simplifyContrastTable	simplifyContrastTable
singleValidMatrix	singleValidMatrix
splitStringToFixedwidthLines	splitStringToFixedwidthLines
static_scatterplot	static_scatterplot
stringsToNamedVector	stringsToNamedVector
summarisematrix	summarisematrix
summarisematrixInput	summarisematrixInput
summarizeMatrix	summarizeMatrix
summarySE	summarySE
ucfirst	ucfirst
unpack.list	unpack.list
upset	upset
upsetInput	upsetInput
upsetOutput	upsetOutput
validate_indices	validate_indices
validate_inputs	validate_inputs
volcanoplot	volcanoplot
volcanoplotInput	volcanoplotInput
volcanoplotOutput	volcanoplotOutput
[,ExploratorySummarizedExperimentList,ANY,missing,ANY-method	ExploratorySummarizedExperimentList-class
[,ExploratorySummarizedExperimentList,logical,missing,ANY-method	ExploratorySummarizedExperimentList-class
[,ExploratorySummarizedExperimentList,numeric,missing,ANY-method	ExploratorySummarizedExperimentList-class
