This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

CellMixS

This is the development version of CellMixS; for the stable release version, see CellMixS.

Evaluate Cellspecific Mixing

Bioconductor version: Development (3.18)

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 uzh.ch>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CellMixS")

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("CellMixS")
Explore data integration and batch effects HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, GeneExpression, SingleCell, Software, Transcriptomics
Version 1.17.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 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
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
System Requirements
Enhances
URL https://github.com/almutlue/CellMixS
Bug Reports https://github.com/almutlue/CellMixS/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CellMixS_1.17.0.tar.gz
Windows Binary CellMixS_1.17.0.zip
macOS Binary (x86_64) CellMixS_1.17.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CellMixS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CellMixS
Bioc Package Browser https://code.bioconductor.org/browse/CellMixS/
Package Short Url https://bioconductor.org/packages/CellMixS/
Package Downloads Report Download Stats