Man pages for pinin4fjords/shinyngs
Shiny apps for NGS data

annotatedHeatmapMake a heatmap with annotations by experimental variable
assaydatatableThe server function of the assaydatatable module
assaydatatableInputThe UI input function of the assaydatatable module
assaydatatableOutputThe output function of the assaydatatable module
barcode_plotMake a gene set barcode plot using Limma
barplotServer function of the 'barplot' module
barplotInputInput function of the 'barplot' module
barplotOutputOutput function of the 'barplot' module
bootstrapMedianBootstrap the standard error of the median
boxplotThe server function of the boxplot module
boxplotInputThe input function of the boxplot module
boxplotOutputThe output function of the boxplot module
calculateDendrogramCalculate a clustering dendgrogram based on correlation
calculateDistCalculate a distance matrix based on correlation
calculatePCAFractionExplainedExtract the percent variance from a PCA analysis
cardinalNumericFieldMake a numeric field with selectable associated cardinality...
chipseqThe server function of the chipseq module. Currently a...
chipseqInputThe input function of the chipseq module. Currently a...
chooseGroupingVariablesChoose a valid set of grouping variables from a targets/...
clusteringThe server function of the clustering module
clusteringDendrogramMake a clustering dendrogram with coloring by experimental...
clusteringInputThe input function of the clustering module
clusteringOutputThe output function of the clustering module
colGeomMeansGeometric means by matrix column
colMediansMedians by matrix column
colormakerThe output function of the colorby module
colormakerInputThe input function of the colorby module
contrastsThe server function of the contrasts module
contrastsInputThe input function of the contrasts module
contrastsOutputThe output function of the contrasts module
convertIdsConvert row names to metadata identifiers
dendroThe server function of the dendrogram module
dendroInputThe input function of the dendrogram module
dendroOutputThe output function of the dendro module
dexseqplotThe server function of the dexseqplot Shiny module
dexseqplotInputThe UI input function of the dexseqplot Shiny module
dexseqplotOutputThe UI output function of the dexseqplot Shiny module....
dexseqtableThe server function of the dexseqtable module
dexseqtableInputThe UI input function of the dexseqtable module
dexseqtableInputFieldsMake input fields for producing a table of differential exon...
dexseqtableOutputThe output function of the dexseqtable module
differentialtableThe server function of the differentialtable module
differentialtableInputThe UI input function of the differentialtable module
differentialtableOutputThe output function of the differentialtable module
eselistFromYAMLBuild an ExploratorySummarisedExperimentList from a YAML...
evaluateCardinalFilterEvaluate a vector of values with respect to a limit and a...
experimenttableThe server function of the experimenttable module
experimenttableInputThe UI input function of the experimenttable module
experimenttableOutputThe output function of the experimenttable module
ExploratorySummarizedExperimentExploratorySummarizedExperiments
ExploratorySummarizedExperiment-classThe ExploratorySummarizedExperiment class
ExploratorySummarizedExperimentListExploratorySummarizedExperimentLists, containers for...
ExploratorySummarizedExperimentList-classThe ExploratorySummaizedExperimentList class
fieldSetsCreate sets of fields for display
foldChangeCalculate fold change between two vectors
foldchangeplotThe server function of the 'foldchangeplot' module
foldchangeplotInputThe UI input function of the 'foldchangeplot' module
foldchangeplotOutputThe output function of the 'foldchangeplot' module
geneThe server function of the gene module
geneBarplotMain function for drawing the bar plot with plotly
geneInputThe input function of the gene module
geneModelPlotMake a gene model plot for a chromosomal location
geneOutputThe input function of the gene module
geneselectThe server function of the geneselect module
geneselectInputThe UI input function of the geneselect module
genesetanalysistableThe server function of the genesetanalysistable module
genesetanalysistableInputThe UI input function of the genesetanalysistable module
genesetanalysistableOutputThe output function of the genesetanalysistable module
genesetbarcodeplotThe server function of the genesetbarcodeplot module
genesetbarcodeplotInputThe UI input function of the genesetbarcodeplot module
genesetbarcodeplotOutputThe output function of the genesetbarcodeplot module
genesetselectThe server function of the genesetselect module
genesetselectInputThe UI function of the genesetselect module
geom_meanGeometric mean
ggplot_boxplotMake a boxplot with coloring by experimental variable
ggplotifyReshape data to the way 'ggplot2' likes it
groupbyThe server function of the groupby module
groupbyInputThe UI function of the groupby module
heatmapThe server function of the heatmap module
heatmapInputThe input function of the heatmap module
heatmapOutputThe output function of the heatmap module
hiddenInputMake a hidden input field. Handy for replacing superfluous...
idToLabelCreate row labels based on the settings of 'labelfield' in...
illuminaarrayThe server function of the illuminaarray module
illuminaarrayInputThe input function of the illuminaarray module
illuminaarrayqcThe server function of the illuminaarrayqc module
illuminaarrayqcInputThe input function of the illuminaarrayqc module
illuminaarrayqcOutputThe output function of the illuminaarrayqc module
inlineFieldWrap a Shiny input so its label is displayed inline
interactiveHeatmapMake a ineractive heatmap with d3heatmap
interleaveColumnsInterleave the columns of two matrices of equal dimensions
labelMatrixAdd columns to display ID and label in a table
labelselectfieldThe server function of the 'labelselectfield' module
labelselectfieldInputThe input function of the 'labelselectfield' module
linkMatrixAdd links to a table
makeAnnotationColorsMake color sets to use in heatmap annotation
makeColorScaleMake a color palette of a specified length
makeContrastControlMake a select field for picking one or more contrasts
makeContrastFilterSetMake a complete set of filters for a contrast: the contrast...
makePackageCitationReturn a usable citation string for a package
maplotThe server function of the 'maplot' module
maplotInputThe UI input function of the 'maplot' module
maplotOutputThe output function of the 'maplot' module
modalInputThe input function for the 'modal' module
modalOutputThe output function of the 'modal' module
na.replaceReplace NAs with a string for convenience
nlinesCount the number of lines in a string
pcaThe server function of the pca module
pcaInputThe input function of the pca module
pcaOutputThe output function of the pca module
plotdownloadThe server function of the gene set module
plotdownloadInputThe input function of the gene plotdownload module
plotly_boxplotMake a boxplot with coloring by experimental variable
plotly_quartilesMake a line-based alternative to boxplots
prepareAppMake UI and server functions for Shiny apps based on data...
prettifyGeneSetNamePrettify gene set names like those from MSigDB
prettifyVariablenameMake machine variable names pretty for display
pushToListSimple list push
readreportsServer function of the 'readreports' module
readreportsInputInput function of the 'readreports' module
readreportsOutputOutput function of the 'readreports' module
rnaseqThe server function of the rnaseq module
rnaseqInputThe input function of the rnaseq module
rowmetatableThe server function of the rowmetatable module
rowmetatableInputThe UI input function of the rowmetatable module
rowmetatableOutputThe output function of the rowmetatable module
runPCARun a simple PCA analysis
sampleselectThe server function of the sampleselect module This module...
sampleselectInputThe UI input function of the sampleselect module
scatterplotServer function for the scatterplot module
scatterplotcontrolsServer function for scatterplotcontrols module
scatterplotcontrolsInputInput function for scatterplotcontrols module
scatterplotInputInput function for the scatterplot module
scatterplotOutputOutput function for the scatterplot module
selectmatrixThe server function of the selectmatrix module
selectmatrixInputThe UI input function of the selectmarix module
shinyngsInteractive downstream analysis with ShinyNGS.
simpleAppProduce a simple app with controls and layout for a single...
simpletableThe server function of the simpletable module
simpletableInputThe UI input function of the simpletable module This module...
simpletableOutputThe output function of the simpletable module
simplifyContrastTableSimplify a contrast table
singleValidMatrixIs there only one matrix to plot from this object?
splitStringToFixedwidthLinesGiven a string with spaces, try to split into multiple lines...
summarisematrixThe server function of the summarisematrix module
summarisematrixInputThe input function of the summarizematrix module
summarizeMatrixSummarise the rows of a matrix, applying a function to groups...
summarySESummarise an input matrix
ucfirstCapitalise the first letter of a string
unpack.listUnpack a list to the environment. Handy when many reactive...
upsetThe server function of the upstart module
upsetInputThe input function of the upset module
upsetOutputThe output function of the clustering module
volcanoplotThe server function of the 'volcanoplot' module
volcanoplotInputThe UI input function of the 'volcanoplot' module
volcanoplotOutputThe output function of the 'volcanoplot' module
pinin4fjords/shinyngs documentation built on Aug. 27, 2017, 9:07 p.m.