Shiny App to Explore RNA-Seq Analysis
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘carnation’ version 0.99.8
Help Pages
-- 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_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 --
| install_carnation | Create carnation python environment |
| in_admin_group | is user is in admin group? |
| is_site_admin | is user an admin? |
-- 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 |
| 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 |
| 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 |