chevreulShiny
This is the development version of chevreulShiny; for the stable release version, see chevreulShiny.
Tools for managing SingleCellExperiment objects as projects
Bioconductor version: Development (3.24)
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]
, Bhavana Bhat [aut]
Maintainer: Kevin Stachelek <kevin.stachelek at gmail.com>
citation("chevreulShiny")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DataImport, DimensionReduction, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics, Visualization |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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 |
See More
| Suggests | BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0), EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86 |
| 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 | chevreulShiny_1.5.0.tar.gz |
| Windows Binary (x86_64) | chevreulShiny_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | chevreulShiny_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | chevreulShiny_1.5.0.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/ |
| Package Downloads Report | Download Stats |