Package: carnation 1.1.0

Apratim Mitra

carnation: Interactive Exploration & Management of RNA-Seq Analyses

Highly interactive & modular shiny app to explore three facets of RNA-Seq analysis: differential expression (DE), functional enrichment and pattern analysis. Several visualizations are implemented to provide a wide-ranging view of data sets. For DE analysis, we provide PCA plot, MA plot, Upset plot & heatmaps, in addition to a highly customizable gene plot. Seven different visualizations are available for functional enrichment analysis, and we also support gene pattern analysis. Genes of interest can be tracked across all modules using the gene scratchpad. In addition, carnation provides an integrated platform to manage multiple projects and user access that can be run on a central server to share with collaborators.

Authors:Apratim Mitra [aut, cre], Matthew Tyler Menold [ctb], Ryan Dale [fnd]

carnation_1.1.0.tar.gz
carnation_1.1.0.zip(r-4.7)carnation_1.1.0.zip(r-4.6)carnation_1.1.0.zip(r-4.5)
carnation_1.1.0.tgz(r-4.6-any)carnation_1.1.0.tgz(r-4.5-any)
carnation_1.1.0.tar.gz(r-4.7-any)carnation_1.1.0.tar.gz(r-4.6-any)
carnation_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
carnation/json (API)
NEWS

# Install 'carnation' in R:
install.packages('carnation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nichd-bspc/carnation/issues

Pkgdown/docs site:https://nichd-bspc.github.io

Datasets:
  • degpatterns_dex - A 'degPatterns' object for differentially expressed genes in the dexamethasone treatment comparison.
  • 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.
  • 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

On BioConductor:carnation-1.1.0(bioc 3.24)carnation-1.0.0(bioc 3.23)

guigeneexpressionsoftwareshinyappsgotranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysgenesetenrichment

5.41 score 2 stars 17 scripts 72 downloads 86 exports 245 dependencies

Last updated from:4789c1f5fd. Checks:1 NOTE, 2 WARNING, 7 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE356
linux-devel-x86_64WARNING598
source / vignettesOK529
linux-release-x86_64OK691
macos-release-arm64OK359
macos-oldrel-arm64OK376
windows-develWARNING488
windows-releaseOK610
windows-oldrelOK585
wasm-releaseOK301

Exports:add_metadataadd.set.columnalluvialServeralluvialUIcheck_user_accesscnetPlotServercnetPlotUIcreate_access_yamldendrogramServerdendrogramUIdistillPlotServerdistillPlotUIdownloadButtonServerdownloadButtonUIenrich_to_genetonicenrichmapServerenrichmapUIenrichServerenrichUIformat_genesfromList.with.namesfuzzyPlotServerfuzzyPlotUIgenePlotServergenePlotUIget_access_pathget_configget_config_pathget_degplotget_gene_countsget_project_name_from_pathget_upset_tableget_y_initgetcountplotgs_radarheatmapServerheatmapUIhelpButtonServerhelpButtonUIhorizonServerhorizonUIin_admin_groupinit_local_configinstall_carnationis_site_adminis_valid_pattern_objloadDataServerloadDataUImake_example_carnation_objectmake_final_objectmakeEnrichResultmaPlotServermaPlotUImaterialize_carnation_objectmetadataServermetadataUImy.summarypatternPlotServerpatternPlotUIpcaPlotServerpcaPlotUIplotMA.labelplotMA.label_lyplotPCA.lyplotPCA.sanplotScatter.labelplotScatter.label_lyradarServerradarUIread_access_yamlrun_carnationsave_access_yamlsaveServersaveUIscatterPlotServerscatterPlotUIset_configsettingsServersettingsUIsummarize_res_listsumovPlotServersumovPlotUItop.genesupsetPlotServerupsetPlotUIvalidate_carnation_object

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassassertthatbackbonebackportsbase64encBHBiasedUrnbillboarderBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbs4DashbslibcacachemcallrcheckmatecigarillocirclizecliclueclusterclusterProfilercodetoolscolorspacecolourpickercommonmarkComplexHeatmapComplexUpsetcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdoParallelDOSEdplyrDTdynamicTreeCuteggenrichitenrichplotevaluateexpmfarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfreshfsfutile.loggerfutile.optionsgclusgdtoolsgeneLenDataBasegenericsGeneTonicGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggridgesggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgoseqgraphgridExtragridGraphicsgsongtableheatmaplyherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallearnrlifecyclelitedownlocfitmagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImosdefnlmeopensslotelpatchworkpermutepillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqapqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLRCurlregistryrenvreshape2restfulrreticulateRhtslibrintrojsrjsonrlangrmarkdownrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesscatterpiescryptSeqinfoseriationshapeshinyshinyAceshinyBSshinycssloadersshinyjsshinymanagershinythemesshinyWidgetssnowsortablesourcetoolsSparseArraySparseMstringistringrSummarizedExperimentsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextippytopGOtreeioTSPtweenrtxdbmakerUCSC.utilsutf8vctrsveganviridisviridisLitevisNetworkwaiterwebshotwithrxfunXMLxml2xtableXVectoryamlyulab.utils

carnation - airway tutorial

Apratim Mitra

Rendered fromcarnation.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-28
Started: 2025-03-13

Readme and manuals

Help Manual

Help pageTopics
Add metadata to counts data frameadd_metadata
Add set column to UpSet plot matrixadd.set.column
Alluvial plot modulealluvialmod alluvialServer alluvialUI
Get data areas a user has access tocheck_user_access
Cnetplot modulecnetmod cnetPlotServer cnetPlotUI
Create access yamlcreate_access_yaml
Pattern plot moduledegmod patternPlotServer patternPlotUI
A 'degPatterns' object for differentially expressed genes in the dexamethasone treatment comparison.degpatterns_dex
Dendrogram moduledendrogramServer dendrogramUI dendromod
Distilled enrichment map moduledistillmod distillPlotServer distillPlotUI
Download button moduledlmod downloadButtonServer downloadButtonUI
Make dummy GeneTonic objectdummy_genetonic
Enrichment map plot moduleemapmod enrichmapServer enrichmapUI
Convert enrichResult to GeneTonic objectenrich_to_genetonic
An 'enrichResult' object for differentially expressed genes in the cell line comparison.eres_cell
An 'enrichResult' object for differentially expressed genes in the dexamethasone treatment comparison.eres_dex
format gene names to look pretty in table outputformat_genes
Prepare list for UpSet plots, but include rownamesfromList.with.names
Functional enrichment moduleenrichServer enrichUI funenrichmod
Fuzzy enrichment map modulefuzzymod fuzzyPlotServer fuzzyPlotUI
Gene plot modulegeneplotmod genePlotServer genePlotUI
Get path to access yaml fileget_access_path
Get configget_config
Get path to local config yaml fileget_config_path
Plot a degPatterns objectget_degplot
Get read counts for geneget_gene_counts
Get project name from pathget_project_name_from_path
Generate upset plot tableget_upset_table
Get initial y-axis limitsget_y_init
Create gene plotgetcountplot
Radar plotgs_radar
Heatmap moduleheatmapmod heatmapServer heatmapUI
Help button modulehelpButtonServer helpButtonUI helpmod
Help modalhelpModal
Horizon plot modulehorizonmod horizonServer horizonUI
is user is in admin group?in_admin_group
Initialize local configinit_local_config
Create carnation python environmentinstall_carnation
is user an admin?is_site_admin
Validate Pattern Analysis Object Schemais_valid_pattern_obj
Load data moduleloadDataServer loadDataUI loadmod
Make example carnation objectmake_example_carnation_object
Make final object for internal use by the appmake_final_object
Make an enrichResult obj from a data framemakeEnrichResult
MA plot modulemaplotmod maPlotServer maPlotUI
Materialize expensive carnation object componentsmaterialize_carnation_object
Metadata modulemetadataServer metadataUI metamod
Summarize DESeq2 results into a dataframemy.summary
PCA plot modulepcamod pcaPlotServer pcaPlotUI
Create a labeled MA plotplotMA.label
Create an interactive labeled MA plotplotMA.label_ly
Plot an interactive PCA plotplotPCA.ly
Adjustable PCA plotplotPCA.san
Plot a scatterplot to compare two contrastsplotScatter.label
Plot an interactive scatterplot to compare two contrastsplotScatter.label_ly
Radar plot moduleradarmod radarServer radarUI
Read access yaml with user groups and data areasread_access_yaml
A 'DESeqResults' object testing the difference between two cell lines of smooth muscle cellsres_cell
A 'DESeqResults' object testing the effect of dexamethasone on smooth muscle cellsres_dex
Carnationrun_carnation
Save access yaml to filesave_access_yaml
Save object module UIsavemod saveServer saveUI
Scatterplot modulescattermod scatterPlotServer scatterPlotUI
Set configset_config
Settings modulesettingsmod settingsServer settingsUI
Combine everything in the results list into a single tablesummarize_res_list
Summary overview plot modulesumovmod sumovPlotServer sumovPlotUI
Get top DE genes by log2FoldChange or adjusted p-valuetop.genes
Upset plot moduleupsetmod upsetPlotServer upsetPlotUI
Validate a carnation objectvalidate_carnation_object