CytoPipelineGUI
This is the released version of CytoPipelineGUI; for the devel version, see CytoPipelineGUI.
GUI's for visualization of flow cytometry data analysis pipelines
Bioconductor version: Release (3.23)
This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.
Author: Philippe Hauchamps [aut, cre]
, Laurent Gatto [aut]
, Dan Lin [ctb]
Maintainer: Philippe Hauchamps <philippe.hauchamps at uclouvain.be>
citation("CytoPipelineGUI")):
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")
BiocManager::install("CytoPipelineGUI")
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("CytoPipelineGUI")| CytoPipelineGUI : visualization of Flow Cytometry Data Analysis Pipelines run with CytoPipeline | HTML | R Script |
| Demonstration of the CytoPipeline R package suite functionalities | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FlowCytometry, GUI, ImmunoOncology, Preprocessing, QualityControl, ShinyApps, Software, Visualization, WorkflowStep |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.4), CytoPipeline(>= 1.9.3) |
| Imports | shiny, plotly, ggplot2, flowCore |
| System Requirements | |
| URL | https://uclouvain-cbio.github.io/CytoPipelineGUI |
| Bug Reports | https://github.com/UCLouvain-CBIO/CytoPipelineGUI/issues |
See More
| Suggests | testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | CytoPipeline |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CytoPipelineGUI_1.10.0.tar.gz |
| Windows Binary (x86_64) | CytoPipelineGUI_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | CytoPipelineGUI_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | CytoPipelineGUI_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CytoPipelineGUI |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CytoPipelineGUI |
| Bioc Package Browser | https://code.bioconductor.org/browse/CytoPipelineGUI/ |
| Package Short Url | https://bioconductor.org/packages/CytoPipelineGUI/ |
| Package Downloads Report | Download Stats |