ExploratorySummarizedExperiment
                        ExploratorySummarizedExperiments
ExploratorySummarizedExperiment-class
                        The ExploratorySummarizedExperiment class
ExploratorySummarizedExperimentList
                        ExploratorySummarizedExperimentLists,
                        containers for ExploratorySummarizedExperiments
ExploratorySummarizedExperimentList-class
                        The ExploratorySummaizedExperimentList class
addPoints               Add points to a plotly object
addTextLabels           Add permanent text labels to points in a plotly
                        graph
adjustLayout            Apply layout adjustments to plotly object
annotatedHeatmap        Make a heatmap with annotations by experimental
                        variable
anova_pca_metadata      Generate a matrix of anova values for
                        associating principal components with
                        categorical covariates.
assaydatatable          The server function of the assaydatatable
                        module
assaydatatableInput     The UI input function of the assaydatatable
                        module
assaydatatableOutput    The output function of the assaydatatable
                        module
barcode_plot            Make a gene set barcode plot using Limma
barplot                 Server function of the 'barplot' module
barplotInput            Input function of the 'barplot' module
barplotOutput           Output function of the 'barplot' module
bootstrapMedian         Bootstrap the standard error of the median
boxplot                 The server function of the boxplot module
boxplotInput            The input function of the boxplot module
boxplotOutput           The output function of the boxplot module
calculateDendrogram     Calculate a clustering dendgrogram based on
                        correlation
calculateDist           Calculate a distance matrix based on
                        correlation
calculatePCAFractionExplained
                        Extract the percent variance from a PCA
                        analysis
cardinalNumericField    Make a numeric field with selectable associated
                        cardinality (>, < ..).
checkListIsSubset       Check one list is a subset of another and throw
                        an error if not
chipseq                 The server function of the chipseq module.
                        Currently a near-clone of the RNA-seq module,
                        with ChIP-seq optimisations planned.
chipseqInput            The input function of the chipseq module.
                        Currently a near-clone of the RNA-seq module,
                        with ChIP-seq optimisations planned.
chooseGroupingVariables
                        Choose a valid set of grouping variables from a
                        targets/ experiment data frame.
clustering              The server function of the clustering module
clusteringDendrogram    Make a clustering dendrogram with coloring by
                        experimental variable
clusteringInput         The input function of the clustering module
clusteringOutput        The output function of the clustering module
colGeomMeans            Geometric means by matrix column
colMedians              Medians by matrix column
colormaker              The output function of the colorby module
colormakerInput         The input function of the colorby module
compilePCAData          Run PCA on a given matrix, expected to be
                        variance stabilised (at least log-transformed)
compile_contrast_data   Compile contrast stats for inclusion in
                        shinyngs
cond_log2_transform_assays
                        Conditionally apply log2 transformation on
                        assay data based on log2_assays parameter.
cond_log2_transform_matrix
                        Apply log2 transformation on a matrix.
contrasts               The server function of the contrasts module
contrastsInput          The input function of the contrasts module
contrastsOutput         The output function of the contrasts module
convertIds              Convert row names to metadata identifiers
dendro                  The server function of the dendrogram module
dendroInput             The input function of the dendrogram module
dendroOutput            The output function of the dendro module
dexseqplot              The server function of the dexseqplot Shiny
                        module
dexseqplotInput         The UI input function of the dexseqplot Shiny
                        module
dexseqplotOutput        The UI output function of the dexseqplot Shiny
                        module. Produces a plot and a table of values.
dexseqtable             The server function of the dexseqtable module
dexseqtableInput        The UI input function of the dexseqtable module
dexseqtableInputFields
                        Make input fields for producing a table of
                        differential exon usage. Separated here for
                        re-use by the dexseqplot module
dexseqtableOutput       The output function of the dexseqtable module
differentialtable       The server function of the differentialtable
                        module
differentialtableInput
                        The UI input function of the differentialtable
                        module
differentialtableOutput
                        The output function of the differentialtable
                        module
drawLines               Overlay lines on a plotly-generated plot
eselistFromYAML         Build an ExploratorySummarisedExperimentList
                        from a YAML description
eselistfromConfig       Build an ExploratorySummarisedExperimentList
                        from a description provided in a list
evaluateCardinalFilter
                        Evaluate a vector of values with respect to a
                        limit and a cardinality, being '>', '<' , '> or
                        <-' (e.g. a fold change above a limit in + or -
                        directions), or '< and >-' (not a above a limit
                        in + or -).
experimenttable         The server function of the experimenttable
                        module
experimenttableInput    The UI input function of the experimenttable
                        module
experimenttableOutput   The output function of the experimenttable
                        module
fieldSets               Create sets of fields for display
foldChange              Calculate fold change between two vectors
foldchangeplot          The server function of the 'foldchangeplot'
                        module
foldchangeplotInput     The UI input function of the 'foldchangeplot'
                        module
foldchangeplotOutput    The output function of the 'foldchangeplot'
                        module
gene                    The server function of the gene module
geneBarplot             Main function for drawing the bar plot with
                        plotly
geneInput               The input function of the gene module
geneModelPlot           Make a gene model plot for a chromosomal
                        location
geneOutput              The input function of the gene module
geneselect              The server function of the geneselect module
geneselectInput         The UI input function of the geneselect module
genesetanalysistable    The server function of the genesetanalysistable
                        module
genesetanalysistableInput
                        The UI input function of the
                        genesetanalysistable module
genesetanalysistableOutput
                        The output function of the genesetanalysistable
                        module
genesetbarcodeplot      The server function of the genesetbarcodeplot
                        module
genesetbarcodeplotInput
                        The UI input function of the genesetbarcodeplot
                        module
genesetbarcodeplotOutput
                        The output function of the genesetbarcodeplot
                        module
genesetselect           The server function of the genesetselect module
genesetselectInput      The UI function of the genesetselect module
geom_mean               Geometric mean
getExtension            Extract the extension of a file
getSeparator            Infer a separator from the extension of an
                        input file
ggplot_boxplot          Make a boxplot with coloring by experimental
                        variable
ggplot_densityplot      Make a static density plot with ggplot2
ggplotify               Reshape data to the way 'ggplot2' likes it
groupby                 The server function of the groupby module
groupbyInput            The UI function of the groupby module
heatmap                 The server function of the heatmap module
heatmapInput            The input function of the heatmap module
heatmapOutput           The output function of the heatmap module
hiddenInput             Make a hidden input field. Handy for replacing
                        superfluous single-value selects etc
idToLabel               Create row labels based on the settings of
                        'labelfield' in the
                        'ExploratorySummarizedExperiment' object and
                        the annotation data in 'mcols'.
illuminaarray           The server function of the illuminaarray module
illuminaarrayInput      The input function of the illuminaarray module
illuminaarrayqc         The server function of the illuminaarrayqc
                        module
illuminaarrayqcInput    The input function of the illuminaarrayqc
                        module
illuminaarrayqcOutput   The output function of the illuminaarrayqc
                        module
inlineField             Wrap a Shiny input so its label is displayed
                        inline
interactiveHeatmap      Make a ineractive heatmap with d3heatmap
interleaveColumns       Interleave the columns of two matrices of equal
                        dimensions
is_valid_positive_integer_vector
                        Check if a comma-separated string can be parsed
                        to an integer vector
labelMatrix             Add columns to display ID and label in a table
labelselectfield        The server function of the 'labelselectfield'
                        module
labelselectfieldInput   The input function of the 'labelselectfield'
                        module
linkMatrix              Add links to a table
madScore                Calculate MAD scores as per OmicSoft
makeAnnotationColors    Make color sets to use in heatmap annotation
makeColorScale          Make a color palette of a specified length
makeContrastControl     Make a select field for picking one or more
                        contrasts
makeContrastFilterSet   Make a complete set of filters for a contrast:
                        the contrast itself, fold change, and where
                        applicable p- and q- values.
makePackageCitation     Return a usable citation string for a package
maplot                  The server function of the 'maplot' module
maplotInput             The UI input function of the 'maplot' module
maplotOutput            The output function of the 'maplot' module
modalInput              The input function for the 'modal' module
modalOutput             The output function of the 'modal' module
na.replace              Replace NAs with a string for convenience
nlines                  Count the number of lines in a string
pca                     The server function of the pca module
pcaInput                The input function of the pca module
pcaOutput               The output function of the pca module
plotdownload            The server function of the gene set module
plotdownloadInput       The input function of the gene plotdownload
                        module
plotly_boxplot          Make a boxplot with coloring by experimental
                        variable
plotly_densityplot      Make a dynamic density plot with plotly
plotly_quartiles        Make a line-based alternative to boxplots
plotly_scatterplot      Make scatterplots with 'plot_ly()'
prepareApp              Make UI and server functions for Shiny apps
                        based on data supplied as modfied
                        SummarizedExperiments
prettifyGeneSetName     Prettify gene set names like those from MSigDB
prettifyVariablename    Make machine variable names pretty for display
pushToList              Simple list push
read_contrasts          Read and validate a contrasts file against
                        sample metadata
read_differential       Read tables of differential statistics
read_matrix             Read an expression matrix file and match to
                        specified samples and features
read_metadata           Read a metadata file
readreports             Server function of the 'readreports' module
readreportsInput        Input function of the 'readreports' module
readreportsOutput       Output function of the 'readreports' module
rnaseq                  The server function of the rnaseq module
rnaseqInput             The input function of the rnaseq module
rowmetatable            The server function of the rowmetatable module
rowmetatableInput       The UI input function of the rowmetatable
                        module
rowmetatableOutput      The output function of the rowmetatable module
runPCA                  Run a simple PCA analysis
sampleselect            The server function of the sampleselect module
sampleselectInput       The UI input function of the sampleselect
                        module
scatterplot             Server function for the scatterplot module
scatterplotInput        Input function for the scatterplot module
scatterplotOutput       Output function for the scatterplot module
scatterplotcontrols     Server function for scatterplotcontrols module
scatterplotcontrolsInput
                        Input function for scatterplotcontrols module
selectVariableGenes     Generate an integer ordering to select the n
                        most variable genes out of a matrix
selectmatrix            The server function of the selectmatrix module
selectmatrixInput       The UI input function of the selectmarix module
shinyngs                Interactive downstream analysis with ShinyNGS.
simpleApp               Produce a simple app with controls and layout
                        for a single module, in a shiny
                        'sideBarLayout()'.
simpleSplit             Convenience interface to strsplit()
simpletable             The server function of the simpletable module
simpletableInput        The UI input function of the simpletable module
simpletableOutput       The output function of the simpletable module
simplifyContrastTable   Simplify a contrast table
singleValidMatrix       Is there only one matrix to plot from this
                        object?
splitStringToFixedwidthLines
                        Given a string with spaces, try to split into
                        multiple lines of < 'linewidth' characters
static_scatterplot      Make scatterplots with 'ggplot()' or
                        'scatterplot3d'
stringsToNamedVector    Take two delimiter-separated strings and
                        generate a named vector
summarisematrix         The server function of the summarisematrix
                        module
summarisematrixInput    The input function of the summarizematrix
                        module
summarizeMatrix         Summarise the rows of a matrix, applying a
                        function to groups of cells defined by a factor
summarySE               Summarise an input matrix
ucfirst                 Capitalise the first letter of a string
unpack.list             Unpack a list to the environment. Handy when
                        many reactive functions are returned by a call
                        to a module's server function
upset                   The server function of the upstart module
upsetInput              The input function of the upset module
upsetOutput             The output function of the clustering module
validate_indices        Validate assay indices based on a given string.
validate_inputs         Call the various read/ validate methods for
                        input data surrounding an experiment
volcanoplot             The server function of the 'volcanoplot' module
volcanoplotInput        The UI input function of the 'volcanoplot'
                        module
volcanoplotOutput       The output function of the 'volcanoplot' module
