Package index • carnation

All functions

add.set.column(): Add set column to UpSet plot matrix
add_metadata(): Add metadata to counts data frame
alluvialUI() alluvialServer(): Alluvial plot module
check_user_access(): Get data areas a user has access to
cnetPlotUI() cnetPlotServer(): Cnetplot module
create_access_yaml(): Create access yaml
patternPlotUI() patternPlotServer(): Pattern plot module
degpatterns_dex: A degPatterns object for differentially expressed genes in the dexamethasone treatment comparison.
dendrogramUI() dendrogramServer(): Dendrogram module
distillPlotUI() distillPlotServer(): Distilled enrichment map module
downloadButtonUI() downloadButtonServer(): Download button module
dummy_genetonic(): Make dummy GeneTonic object
enrichmapUI() enrichmapServer(): Enrichment map plot module
enrich_to_genetonic(): Convert enrichResult to GeneTonic object
eres_cell: An enrichResult object for differentially expressed genes in the cell line comparison.
eres_dex: An enrichResult object for differentially expressed genes in the dexamethasone treatment comparison.
format_genes(): format gene names to look pretty in table output
fromList.with.names(): Prepare list for UpSet plots, but include rownames
enrichUI() enrichServer(): Functional enrichment module
fuzzyPlotUI() fuzzyPlotServer(): Fuzzy enrichment map module
genePlotUI() genePlotServer(): Gene plot module
get_access_path(): Get path to access yaml file
get_config(): Get config
get_degplot(): Plot a degPatterns object
get_gene_counts(): Get read counts for gene
get_project_name_from_path(): Get project name from path
get_upset_table(): Generate upset plot table
get_y_init(): Get initial y-axis limits
getcountplot(): Create gene plot
gs_radar(): Radar plot
heatmapUI() heatmapServer(): Heatmap module
helpModal(): Help modal
helpButtonUI() helpButtonServer(): Help button module
horizonUI() horizonServer(): Horizon plot module
in_admin_group(): is user is in admin group?
install_carnation(): Create carnation python environment
is_site_admin(): is user an admin?
loadDataUI() loadDataServer(): Load data module
makeEnrichResult(): Make an enrichResult obj from a data frame
make_example_carnation_object(): Make example carnation object
make_final_object(): Make final object for internal use by the app
maPlotUI() maPlotServer(): MA plot module
metadataUI() metadataServer(): Metadata module
my.summary(): Summarize DESeq2 results into a dataframe
pcaPlotUI() pcaPlotServer(): PCA plot module
plotMA.label(): Create a labeled MA plot
plotMA.label_ly(): Create an interactive labeled MA plot
plotPCA.ly(): Plot an interactive PCA plot
plotPCA.san(): Adjustable PCA plot
plotScatter.label(): Plot a scatterplot to compare two contrasts
plotScatter.label_ly(): Plot an interactive scatterplot to compare two contrasts
radarUI() radarServer(): Radar plot module
read_access_yaml(): Read access yaml with user groups and data areas
res_cell: A DESeqResults object testing the difference between two cell lines of smooth muscle cells
res_dex: A DESeqResults object testing the effect of dexamethasone on smooth muscle cells
run_carnation(): Carnation
save_access_yaml(): Save access yaml to file
saveUI() saveServer(): Save object module UI
scatterPlotUI() scatterPlotServer(): Scatterplot module
settingsUI() settingsServer(): Settings module
summarize.res.list(): Combine everything in the results list into a single table
sumovPlotUI() sumovPlotServer(): Summary overview plot module
top.genes(): Get top DE genes by log2FoldChange or adjusted p-value
upsetPlotUI() upsetPlotServer(): Upset plot module