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Evaluate Cellspecific Mixing

Bioconductor version: Release (3.19)

CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level.

Author: Almut Lütge [aut, cre]

Maintainer: Almut Lütge <almut.luetge at>

Citation (from within R, enter citation("CellMixS")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Explore data integration and batch effects HTML R Script
Reference Manual PDF


biocViews BatchEffect, GeneExpression, SingleCell, Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL (>=2)
Depends kSamples, R (>= 4.0)
Imports BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics
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Suggests BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
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Follow Installation instructions to use this package in your R session.

Source Package CellMixS_1.20.0.tar.gz
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macOS Binary (x86_64) CellMixS_1.20.0.tgz
macOS Binary (arm64) CellMixS_1.20.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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