chevreulShiny

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see chevreulShiny.

Tools for managing SingleCellExperiment objects as projects

Bioconductor version: 3.21

Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Author: Kevin Stachelek [aut, cre] ORCID iD ORCID: 0000-0003-2085-695X , Bhavana Bhat [aut]

Maintainer: Kevin Stachelek <kevin.stachelek at gmail.com>

Citation (from within R, enter citation("chevreulShiny")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("chevreulShiny")

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("chevreulShiny")

Preprocessing HTML R Script

Shiny App HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataImport, DimensionReduction, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics, Visualization

Version 1.0.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License MIT + file LICENSE

Depends R (>= 4.5.0), SingleCellExperiment, shiny (>= 1.6.0), shinydashboard, chevreulProcess, chevreulPlot

Imports alabaster.base, clustree, ComplexHeatmap, DataEditR (>= 0.0.9), DBI, dplyr, DT, EnhancedVolcano, fs, future, ggplot2, ggplotify, grDevices, methods, patchwork, plotly, purrr, rappdirs, readr, RSQLite, S4Vectors, scales, shinyFiles, shinyhelper, shinyjs, shinyWidgets, stats, stringr, tibble, tidyr, tidyselect, utils, waiter, wiggleplotr

System Requirements

URL https://github.com/whtns/chevreulShiny https://whtns.github.io/chevreulShiny/

Bug Reports https://github.com/cobriniklab/chevreulShiny/issues

Suggests BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0), EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86

Linking To

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chevreulShiny_1.0.0.tar.gz

Windows Binary (x86_64) chevreulShiny_1.0.0.zip

macOS Binary (x86_64) chevreulShiny_1.0.0.tgz

macOS Binary (arm64) chevreulShiny_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/chevreulShiny

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chevreulShiny

Bioc Package Browser https://code.bioconductor.org/browse/chevreulShiny/

Package Short Url https://bioconductor.org/packages/chevreulShiny/

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