cydar
Using Mass Cytometry for Differential Abundance Analyses
Bioconductor version: Release (3.20)
Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("cydar")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cydar")
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("cydar")| Detecting differential abundance | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FlowCytometry, ImmunoOncology, MultipleComparison, Proteomics, SingleCell, Software |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 years) |
| License | GPL-3 |
| Depends | SingleCellExperiment |
| Imports | viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors |
| System Requirements | C++11 |
| URL |
See More
| Suggests | ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats |
| Linking To | Rcpp |
| 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 | cydar_1.30.0.tar.gz |
| Windows Binary (x86_64) | cydar_1.30.0.zip |
| macOS Binary (x86_64) | cydar_1.30.0.tgz |
| macOS Binary (arm64) | cydar_1.29.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cydar |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cydar |
| Bioc Package Browser | https://code.bioconductor.org/browse/cydar/ |
| Package Short Url | https://bioconductor.org/packages/cydar/ |
| Package Downloads Report | Download Stats |