carnation
Interactive Exploration & Management of RNA-Seq Analyses
Bioconductor version: 3.24 · Package version: 1.1.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("carnation")Details
| Maintainer | Apratim Mitra <apratim.mitra@gmail.com> |
| Author | Apratim Mitra [aut, cre] (ORCID: <https://orcid.org/0000-0003-3279-0054>), Matthew Tyler Menold [ctb] (ORCID: <https://orcid.org/0009-0007-4728-2470>), Ryan Dale [fnd] (ORCID: <https://orcid.org/0000-0003-2664-3744>) |
| License | MIT + file LICENSE |
| URL | https://nichd-bspc.github.io/carnation/ |
| Bug Reports | https://github.com/NICHD-BSPC/carnation/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ShinyApps, Software, Transcription, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/carnation/ |
Citation
From within R, enter citation("carnation"):
Apratim Mitra. carnation: Interactive Exploration & Management of RNA-Seq Analyses. doi:10.18129/B9.bioc.carnation, R package version 1.1.1, https://bioconductor.org/packages/carnation.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | carnation_1.1.1.tar.gz |
| Windows binary (x86_64) | carnation_1.1.1.zip |
| macOS binary (arm64) | carnation_1.1.1.tgz |
| macOS binary (x86_64) | carnation_1.1.1.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocParallel, colorspace, ComplexUpset, dendextend, DESeq2, dplyr, DT, enrichplot, GeneTonic, ggplot2, ggrepel, heatmaply, htmltools, igraph, methods, MatrixGenerics, plotly, reticulate, RColorBrewer, rintrojs, scales, shiny, shinyBS, shinycssloaders, shinymanager, shinythemes, shinyWidgets, sortable, SummarizedExperiment, tools, utils, viridisLite, visNetwork, yaml
Suggests: airway, BiocStyle, DEGreport, GenomicFeatures, goseq, knitr, org.Hs.eg.db, rmarkdown, testthat