# Interactive Exploration & Management of RNA-Seq Analyses

## Documentation for package ‘carnation’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F G H I L M P R S T U V

## -- A --

add.set.column | Add set column to UpSet plot matrix
add_metadata | Add metadata to counts data frame
alluvialmod | Alluvial plot module
alluvialServer | Alluvial plot module
alluvialUI | Alluvial plot module

## -- C --

check_user_access | Get data areas a user has access to
cnetmod | Cnetplot module
cnetPlotServer | Cnetplot module
cnetPlotUI | Cnetplot module
create_access_yaml | Create access yaml

## -- D --

degmod | Pattern plot module
degpatterns_dex | A 'degPatterns' object for differentially expressed genes in the dexamethasone treatment comparison.
dendrogramServer | Dendrogram module
dendrogramUI | Dendrogram module
dendromod | Dendrogram module
distillmod | Distilled enrichment map module
distillPlotServer | Distilled enrichment map module
distillPlotUI | Distilled enrichment map module
dlmod | Download button module
downloadButtonServer | Download button module
downloadButtonUI | Download button module
dummy_genetonic | Make dummy GeneTonic object

## -- E --

emapmod | Enrichment map plot module
enrichmapServer | Enrichment map plot module
enrichmapUI | Enrichment map plot module
enrichServer | Functional enrichment module
enrichUI | Functional enrichment 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.

## -- F --

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
fuzzyPlotServer | Fuzzy enrichment map module
fuzzyPlotUI | Fuzzy enrichment map module

## -- G --

geneplotmod | Gene plot module
genePlotServer | Gene plot module
genePlotUI | Gene plot module
getcountplot | Create gene plot
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
gs_radar | Radar plot

## -- H --

heatmapmod | Heatmap module
heatmapServer | Heatmap module
heatmapUI | Heatmap module
helpButtonServer | Help button module
helpButtonUI | Help button module
helpmod | Help button module
helpModal | Help modal
horizonmod | Horizon plot module
horizonServer | Horizon plot module
horizonUI | Horizon plot module

## -- I --

init_local_config | Initialize local config
install_carnation | Create carnation python environment
in_admin_group | is user is in admin group?
is_site_admin | is user an admin?
is_valid_pattern_obj | Validate Pattern Analysis Object Schema

## -- L --

loadDataServer | Load data module
loadDataUI | Load data module
loadmod | Load data module

## -- M --

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
maPlotServer | MA plot module
maPlotUI | MA plot module
materialize_carnation_object | Materialize expensive carnation object components
metadataServer | Metadata module
metadataUI | Metadata module
metamod | Metadata module
my.summary | Summarize DESeq2 results into a dataframe

## -- P --

patternPlotServer | Pattern plot module
patternPlotUI | Pattern plot module
pcamod | PCA plot module
pcaPlotServer | PCA plot module
pcaPlotUI | 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

## -- R --

radarmod | Radar plot module
radarServer | Radar plot module
radarUI | 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

## -- S --

savemod | Save object module UI
saveServer | Save object module UI
saveUI | Save object module UI
save_access_yaml | Save access yaml to file
scattermod | Scatterplot module
scatterPlotServer | Scatterplot module
scatterPlotUI | Scatterplot module
settingsmod | Settings module
settingsServer | Settings module
settingsUI | Settings module
set_config | Set config
summarize_res_list | Combine everything in the results list into a single table
sumovmod | Summary overview plot module
sumovPlotServer | Summary overview plot module
sumovPlotUI | Summary overview plot module

## -- T --

top.genes | Get top DE genes by log2FoldChange or adjusted p-value

## -- U --

upsetmod | Upset plot module
upsetPlotServer | Upset plot module
upsetPlotUI | Upset plot module

## -- V --

validate_carnation_object | Validate a carnation object