add.set.column          Add set column to UpSet plot matrix
add_metadata            Add metadata to counts data frame
alluvialmod             Alluvial plot module
check_user_access       Get data areas a user has access to
cnetmod                 Cnetplot module
create_access_yaml      Create access yaml
degmod                  Pattern plot module
degpatterns_dex         A 'degPatterns' object for differentially
                        expressed genes in the dexamethasone treatment
                        comparison.
dendromod               Dendrogram module
distillmod              Distilled enrichment map module
dlmod                   Download button module
dummy_genetonic         Make dummy GeneTonic object
emapmod                 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
funenrichmod            Functional enrichment module
fuzzymod                Fuzzy enrichment map module
geneplotmod             Gene plot module
get_access_path         Get path to access yaml file
get_config              Get config
get_config_path         Get path to local config yaml file
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
heatmapmod              Heatmap module
helpModal               Help modal
helpmod                 Help button module
horizonmod              Horizon plot module
in_admin_group          is user is in admin group?
init_local_config       Initialize local config
install_carnation       Create carnation python environment
is_site_admin           is user an admin?
is_valid_pattern_obj    Validate Pattern Analysis Object Schema
loadmod                 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
maplotmod               MA plot module
materialize_carnation_object
                        Materialize expensive carnation object
                        components
metamod                 Metadata module
my.summary              Summarize DESeq2 results into a dataframe
pcamod                  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
radarmod                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
savemod                 Save object module UI
scattermod              Scatterplot module
set_config              Set config
settingsmod             Settings module
summarize_res_list      Combine everything in the results list into a
                        single table
sumovmod                Summary overview plot module
top.genes               Get top DE genes by log2FoldChange or adjusted
                        p-value
upsetmod                Upset plot module
validate_carnation_object
                        Validate a carnation object
