Files in pinin4fjords/shinyngs
Shiny apps for NGS data
.Rbuildignore
.github/.gitignore
.github/workflows/check-release.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/ExploratorySummarizedExperiment-class.R
R/ExploratorySummarizedExperimentList-class.R
R/accessory.R
R/apps.R
R/assaydatatable.R
R/barplot.R
R/boxplot.R
R/chipseq.R
R/clustering.R
R/colormaker.R
R/contrasts.R
R/dendro.R
R/dexseqplot.R
R/dexseqtable.R
R/differentialtable.R
R/experimenttable.R
R/foldchangeplot.R
R/gene.R
R/geneselect.R
R/genesetanalysistable.R
R/genesetbarcodeplot.R
R/genesetselect.R
R/groupby.R
R/heatmap.R
R/illuminaarray.R
R/illuminaarrayqc.R
R/labelselectfield.R
R/maplot.R
R/modal.R
R/pca.R
R/plotdownload.R
R/readreports.R
R/rnaseq.R
R/rowmetatable.R
R/sampleselect.R
R/scatterplot.R
R/scatterplotcontrols.R
R/selectmatrix.R
R/shinyngs.R
R/simpletable.R
R/summarisematrix.R
R/upset.R
R/volcanoplot.R
README.Rmd
README.md
exec/differential_plots.R
exec/exploratory_plots.R
exec/make_app_from_files.R
exec/validate_fom_components.R
inst/inlinehelp/assaydatatable.md
inst/inlinehelp/boxplot.md
inst/inlinehelp/clustering.md
inst/inlinehelp/clusteringheatmap.md
inst/inlinehelp/dendro.md
inst/inlinehelp/dexseqplot.md
inst/inlinehelp/dexseqtable.md
inst/inlinehelp/differentialtable.md
inst/inlinehelp/experimenttable.md
inst/inlinehelp/expressionheatmap.md
inst/inlinehelp/foldchangeplot.md
inst/inlinehelp/genesetanalysistable.md
inst/inlinehelp/genesetbarcodeplot.md
inst/inlinehelp/illuminaarrayqc.md
inst/inlinehelp/maplot.md
inst/inlinehelp/pca.md
inst/inlinehelp/pcavsexperiment.md
inst/inlinehelp/readreports.md
inst/inlinehelp/rowmetatable.md
inst/inlinehelp/upset.md
inst/inlinehelp/volcanoplot.md
inst/www/shinyngs.css
man/ExploratorySummarizedExperiment-class.Rd
man/ExploratorySummarizedExperiment.Rd
man/ExploratorySummarizedExperimentList-class.Rd
man/ExploratorySummarizedExperimentList.Rd
man/addPoints.Rd
man/addTextLabels.Rd
man/adjustLayout.Rd
man/annotatedHeatmap.Rd
man/anova_pca_metadata.Rd
man/assaydatatable.Rd
man/assaydatatableInput.Rd
man/assaydatatableOutput.Rd
man/barcode_plot.Rd
man/barplot.Rd
man/barplotInput.Rd
man/barplotOutput.Rd
man/bootstrapMedian.Rd
man/boxplot.Rd
man/boxplotInput.Rd
man/boxplotOutput.Rd
man/calculateDendrogram.Rd
man/calculateDist.Rd
man/calculatePCAFractionExplained.Rd
man/cardinalNumericField.Rd
man/checkListIsSubset.Rd
man/chipseq.Rd
man/chipseqInput.Rd
man/chooseGroupingVariables.Rd
man/clustering.Rd
man/clusteringDendrogram.Rd
man/clusteringInput.Rd
man/clusteringOutput.Rd
man/colGeomMeans.Rd
man/colMedians.Rd
man/colormaker.Rd
man/colormakerInput.Rd
man/compilePCAData.Rd
man/compile_contrast_data.Rd
man/cond_log2_transform_assays.Rd
man/cond_log2_transform_matrix.Rd
man/contrasts.Rd
man/contrastsInput.Rd
man/contrastsOutput.Rd
man/convertIds.Rd
man/dendro.Rd
man/dendroInput.Rd
man/dendroOutput.Rd
man/dexseqplot.Rd
man/dexseqplotInput.Rd
man/dexseqplotOutput.Rd
man/dexseqtable.Rd
man/dexseqtableInput.Rd
man/dexseqtableInputFields.Rd
man/dexseqtableOutput.Rd
man/differentialtable.Rd
man/differentialtableInput.Rd
man/differentialtableOutput.Rd
man/drawLines.Rd
man/eselistFromYAML.Rd
man/eselistfromConfig.Rd
man/evaluateCardinalFilter.Rd
man/experimenttable.Rd
man/experimenttableInput.Rd
man/experimenttableOutput.Rd
man/fieldSets.Rd
man/foldChange.Rd
man/foldchangeplot.Rd
man/foldchangeplotInput.Rd
man/foldchangeplotOutput.Rd
man/gene.Rd
man/geneBarplot.Rd
man/geneInput.Rd
man/geneModelPlot.Rd
man/geneOutput.Rd
man/geneselect.Rd
man/geneselectInput.Rd
man/genesetanalysistable.Rd
man/genesetanalysistableInput.Rd
man/genesetanalysistableOutput.Rd
man/genesetbarcodeplot.Rd
man/genesetbarcodeplotInput.Rd
man/genesetbarcodeplotOutput.Rd
man/genesetselect.Rd
man/genesetselectInput.Rd
man/geom_mean.Rd
man/getExtension.Rd
man/getSeparator.Rd
man/ggplot_boxplot.Rd
man/ggplot_densityplot.Rd
man/ggplotify.Rd
man/groupby.Rd
man/groupbyInput.Rd
man/heatmap.Rd
man/heatmapInput.Rd
man/heatmapOutput.Rd
man/hiddenInput.Rd
man/idToLabel.Rd
man/illuminaarray.Rd
man/illuminaarrayInput.Rd
man/illuminaarrayqc.Rd
man/illuminaarrayqcInput.Rd
man/illuminaarrayqcOutput.Rd
man/inlineField.Rd
man/interactiveHeatmap.Rd
man/interleaveColumns.Rd
man/is_valid_positive_integer_vector.Rd
man/labelMatrix.Rd
man/labelselectfield.Rd
man/labelselectfieldInput.Rd
man/linkMatrix.Rd
man/madScore.Rd
man/makeAnnotationColors.Rd
man/makeColorScale.Rd
man/makeContrastControl.Rd
man/makeContrastFilterSet.Rd
man/makePackageCitation.Rd
man/maplot.Rd
man/maplotInput.Rd
man/maplotOutput.Rd
man/modalInput.Rd
man/modalOutput.Rd
man/na.replace.Rd
man/nlines.Rd
man/pca.Rd
man/pcaInput.Rd
man/pcaOutput.Rd
man/plotdownload.Rd
man/plotdownloadInput.Rd
man/plotly_boxplot.Rd
man/plotly_densityplot.Rd
man/plotly_quartiles.Rd
man/plotly_scatterplot.Rd
man/prepareApp.Rd
man/prettifyGeneSetName.Rd
man/prettifyVariablename.Rd
man/pushToList.Rd
man/read_contrasts.Rd
man/read_differential.Rd
man/read_matrix.Rd
man/read_metadata.Rd
man/readreports.Rd
man/readreportsInput.Rd
man/readreportsOutput.Rd
man/rnaseq.Rd
man/rnaseqInput.Rd
man/rowmetatable.Rd
man/rowmetatableInput.Rd
man/rowmetatableOutput.Rd
man/runPCA.Rd
man/sampleselect.Rd
man/sampleselectInput.Rd
man/scatterplot.Rd
man/scatterplotInput.Rd
man/scatterplotOutput.Rd
man/scatterplotcontrols.Rd
man/scatterplotcontrolsInput.Rd
man/selectVariableGenes.Rd
man/selectmatrix.Rd
man/selectmatrixInput.Rd
man/shinyngs.Rd
man/simpleApp.Rd
man/simpleSplit.Rd
man/simpletable.Rd
man/simpletableInput.Rd
man/simpletableOutput.Rd
man/simplifyContrastTable.Rd
man/singleValidMatrix.Rd
man/splitStringToFixedwidthLines.Rd
man/static_scatterplot.Rd
man/stringsToNamedVector.Rd
man/summarisematrix.Rd
man/summarisematrixInput.Rd
man/summarizeMatrix.Rd
man/summarySE.Rd
man/ucfirst.Rd
man/unpack.list.Rd
man/upset.Rd
man/upsetInput.Rd
man/upsetOutput.Rd
man/validate_indices.Rd
man/validate_inputs.Rd
man/volcanoplot.Rd
man/volcanoplotInput.Rd
man/volcanoplotOutput.Rd
screenshots/gene_page.png
tests/testthat.R
tests/testthat/test-accessory.R
vignettes/._gene_page.png
vignettes/gene_page.png
vignettes/pca_highlighted.png
vignettes/shinyngs.R
vignettes/shinyngs.Rmd
vignettes/shinyngs.html
