carnation
This is the development version of carnation; to use it, please install the devel version of Bioconductor.
Interactive Exploration & Management of RNA-Seq Analyses
Bioconductor version: Development (3.23)
This package provides a 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.
Author: Apratim Mitra [aut, cre]
, Matthew Tyler Menold [ctb]
, Ryan Dale [fnd]
Maintainer: Apratim Mitra <apratim.mitra at nih.gov>
citation("carnation")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("carnation")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("carnation")| carnation - airway tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ShinyApps, Software, Transcription, Transcriptomics, Visualization |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| 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 |
| System Requirements | |
| URL | https://nichd-bspc.github.io/carnation/ |
| Bug Reports | https://github.com/NICHD-BSPC/carnation/issues |
See More
| Suggests | airway, BiocStyle, DEGreport, GenomicFeatures, goseq, knitr, org.Hs.eg.db, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | carnation_0.99.9.tar.gz |
| Windows Binary (x86_64) | carnation_0.99.8.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | carnation_0.99.9.tgz |
| macOS Binary (sonoma-arm64) | carnation_0.99.8.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/carnation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/carnation |
| Bioc Package Browser | https://code.bioconductor.org/browse/carnation/ |
| Package Short Url | https://bioconductor.org/packages/carnation/ |
| Package Downloads Report | Download Stats |