carnation
This is the development version of carnation; to use it, please install the devel version of Bioconductor.
Shiny App to Explore RNA-Seq Analysis
Bioconductor version: Development (3.23)
Interactive Shiny dashboard app that can be used to explore RNA-Seq analysis results including 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. In addition, the app provides a platform to manage multiple projects and user groups that can be run on a central server.
Author: Apratim Mitra [aut, cre]
, 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 |
Details
| biocViews | DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ShinyApps, Software, Transcription, Transcriptomics, Visualization |
| Version | 0.99.8 |
| 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_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |