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✨
DESCRIPTION |NEWS
card.svg |card.png
carnation/json (API)

# 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)

gui geneexpression software shinyapps go transcription transcriptomics visualization differentialexpression pathways genesetenrichment

5.41 score 2 stars 17 scripts 86 exports 245 dependencies

Last updated from:4789c1f5fd. Checks:1 NOTE, 2 WARNING, 6 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	361
linux-devel-x86_64	WARNING	671
source / vignettes	OK	523
linux-release-x86_64	OK	664
macos-release-arm64	OK	546
macos-oldrel-arm64	OK	525
windows-devel	WARNING	711
windows-release	OK	629
windows-oldrel	ERROR	630
wasm-release	OK	352

Exports:add_metadata add.set.column alluvialServer alluvialUI check_user_access cnetPlotServer cnetPlotUI create_access_yaml dendrogramServer dendrogramUI distillPlotServer distillPlotUI downloadButtonServer downloadButtonUI enrich_to_genetonic enrichmapServer enrichmapUI enrichServer enrichUI format_genes fromList.with.names fuzzyPlotServer fuzzyPlotUI genePlotServer genePlotUI get_access_path get_config get_config_path get_degplot get_gene_counts get_project_name_from_path get_upset_table get_y_init getcountplot gs_radar heatmapServer heatmapUI helpButtonServer helpButtonUI horizonServer horizonUI in_admin_group init_local_config install_carnation is_site_admin is_valid_pattern_obj loadDataServer loadDataUI make_example_carnation_object make_final_object makeEnrichResult maPlotServer maPlotUI materialize_carnation_object metadataServer metadataUI my.summary patternPlotServer patternPlotUI pcaPlotServer pcaPlotUI plotMA.label plotMA.label_ly plotPCA.ly plotPCA.san plotScatter.label plotScatter.label_ly radarServer radarUI read_access_yaml run_carnation save_access_yaml saveServer saveUI scatterPlotServer scatterPlotUI set_config settingsServer settingsUI summarize_res_list sumovPlotServer sumovPlotUI top.genes upsetPlotServer upsetPlotUI validate_carnation_object

Dependencies:abind aisdk AnnotationDbi ape aplot askpass assertthat backbone backports base64enc BH BiasedUrn billboarder Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bs4Dash bslib ca cachem callr checkmate cigarillo circlize cli clue cluster clusterProfiler codetools colorspace colourpicker commonmark ComplexHeatmap ComplexUpset cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend DESeq2 digest doParallel DOSE dplyr DT dynamicTreeCut egg enrichit enrichplot evaluate expm farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver foreach formatR fresh fs futile.logger futile.options gclus gdtools geneLenDataBase generics GeneTonic GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggridges ggtangle ggtree GlobalOptions glue GO.db GOSemSim goseq graph gridExtra gridGraphics gson gtable heatmaply here highr hms htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval learnr lifecycle litedown locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI mosdef nlme openssl otel patchwork permute pillar pkgconfig plotly plyr png polyclip prettyunits processx progress promises ps purrr qap qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppTOML RCurl registry renv reshape2 restfulr reticulate Rhtslib rintrojs rjson rlang rmarkdown rprojroot Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales scatterpie scrypt Seqinfo seriation shape shiny shinyAce shinyBS shinycssloaders shinyjs shinymanager shinythemes shinyWidgets snow sortable sourcetools SparseArray SparseM stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex tippy topGO treeio TSP tweenr txdbmaker UCSC.utils utf8 vctrs vegan viridis viridisLite visNetwork waiter webshot withr xfun XML xml2 xtable XVector yaml yulab.utils

carnation - airway tutorial

Rendered fromcarnation.Rmdusingknitr::rmarkdown

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

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

Package: carnation 1.1.0

carnation: Interactive Exploration & Management of RNA-Seq Analyses

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