diffcyt
This is the development version of diffcyt; for the stable release version, see diffcyt.
Differential discovery in high-dimensional cytometry via high-resolution clustering
Bioconductor version: Development (3.21)
Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.
Author: Lukas M. Weber [aut, cre] (ORCID:
Maintainer: Lukas M. Weber <lmweberedu at gmail.com>
citation("diffcyt")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("diffcyt")
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("diffcyt")| diffcyt workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.4.0) |
| Imports | flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid |
| System Requirements | |
| URL | https://github.com/lmweber/diffcyt |
| Bug Reports | https://github.com/lmweber/diffcyt/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST |
| Linking To | |
| Enhances | |
| Depends On Me | censcyt, cytofWorkflow |
| Imports Me | treeclimbR, treekoR |
| Suggests Me | CATALYST, tidytof |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | diffcyt_1.27.0.tar.gz |
| Windows Binary (x86_64) | diffcyt_1.27.0.zip (64-bit only) |
| macOS Binary (x86_64) | diffcyt_1.27.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/diffcyt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/diffcyt |
| Bioc Package Browser | https://code.bioconductor.org/browse/diffcyt/ |
| Package Short Url | https://bioconductor.org/packages/diffcyt/ |
| Package Downloads Report | Download Stats |