Man pages for pinin4fjords/shinyngs
Shiny apps for NGS data
| 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... |
| 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... |
| chipseq | The server function of the chipseq module. Currently a... |
| chipseqInput | The input function of the chipseq module. Currently a... |
| chooseGroupingVariables | Choose a valid set of grouping variables from a targets/... |
| clustering | The server function of the clustering module |
| clusteringDendrogram | Make a clustering dendrogram with coloring by experimental... |
| 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 |
| compile_contrast_data | Compile contrast stats for inclusion in shinyngs |
| compilePCAData | Run PCA on a given matrix, expected to be variance stabilised... |
| cond_log2_transform_assays | Conditionally apply log2 transformation on assay data based... |
| 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.... |
| 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... |
| 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 |
| eselistfromConfig | Build an ExploratorySummarisedExperimentList from a... |
| eselistFromYAML | Build an ExploratorySummarisedExperimentList from a YAML... |
| evaluateCardinalFilter | Evaluate a vector of values with respect to a limit and a... |
| 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... |
| ExploratorySummarizedExperimentList-class | The ExploratorySummaizedExperimentList class |
| 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... |
| idToLabel | Create row labels based on the settings of 'labelfield' in... |
| 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... |
| 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... |
| 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... |
| 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... |
| 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 |
| 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 |
| selectVariableGenes | Generate an integer ordering to select the n most variable... |
| shinyngs | Interactive downstream analysis with ShinyNGS. |
| simpleApp | Produce a simple app with controls and layout for a single... |
| 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... |
| static_scatterplot | Make scatterplots with 'ggplot()' or 'scatterplot3d' |
| stringsToNamedVector | Take two delimiter-separated strings and generate a named... |
| 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... |
| 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... |
| 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... |
| 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 |
