CytoMDS
This is the development version of CytoMDS; for the stable release version, see CytoMDS.
Low Dimensions projection of cytometry samples
Bioconductor version: Development (3.24)
This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.
Author: Philippe Hauchamps [aut, cre]
, Laurent Gatto [aut]
, Dan Lin [ctb]
Maintainer: Philippe Hauchamps <philippe.hauchamps at uclouvain.be>
citation("CytoMDS")):
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("CytoMDS")
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("CytoMDS")| Low Dimensional Projection of Cytometry Samples | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction, FlowCytometry, MultidimensionalScaling, QualityControl, Software, Visualization |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.4), Biobase |
| Imports | methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline |
| System Requirements | |
| URL | https://uclouvain-cbio.github.io/CytoMDS |
| Bug Reports | https://github.com/UCLouvain-CBIO/CytoMDS/issues |
See More
| Suggests | testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MDSvis |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CytoMDS_1.9.0.tar.gz |
| Windows Binary (x86_64) | CytoMDS_1.9.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CytoMDS_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | CytoMDS_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CytoMDS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CytoMDS |
| Bioc Package Browser | https://code.bioconductor.org/browse/CytoMDS/ |
| Package Short Url | https://bioconductor.org/packages/CytoMDS/ |
| Package Downloads Report | Download Stats |