# Shiny apps for NGS data

## Documentation for package ‘shinyngs’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N P R S U V

shinyngs-package | Interactive downstream analysis with ShinyNGS.

## -- A --

annotatedHeatmap | Make a heatmap with annotations by experimental variable
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

## -- B --

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

## -- C --

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 (>, < ..).
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
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

## -- D --

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

## -- E --

eselistFromYAML | Build an ExploratorySummarisedExperimentList from a YAML description
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
ExploratorySummarizedExperiment | ExploratorySummarizedExperiments
ExploratorySummarizedExperiment-class | The ExploratorySummarizedExperiment class
ExploratorySummarizedExperimentList | ExploratorySummarizedExperimentLists, containers for ExploratorySummarizedExperiments
ExploratorySummarizedExperimentList-class | The ExploratorySummaizedExperimentList class

## -- F --

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

## -- G --

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
ggplotify | Reshape data to the way 'ggplot2' likes it
ggplot_boxplot | Make a boxplot with coloring by experimental variable
groupby | The server function of the groupby module
groupbyInput | The UI function of the groupby module

## -- H --

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

## -- I --

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

## -- L --

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

## -- M --

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

## -- N --

na.replace | Replace NAs with a string for convenience
nlines | Count the number of lines in a string

## -- P --

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_quartiles | Make a line-based alternative to boxplots
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

## -- R --

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

## -- S --

sampleselect | The server function of the sampleselect module This module provides controls for selecting matrix columns by sample or group name.
sampleselectInput | The UI input function of the sampleselect module
scatterplot | Server function for the scatterplot module
scatterplotcontrols | Server function for scatterplotcontrols module
scatterplotcontrolsInput | Input function for scatterplotcontrols module
scatterplotInput | Input function for the scatterplot module
scatterplotOutput | Output function for the scatterplot module
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()'.
simpletable | The server function of the simpletable module
simpletableInput | The UI input function of the simpletable module This module produces a simple datatable output with a download button.
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
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

## -- U --

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

## -- V --

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