CellMixS

This is the released version of CellMixS; for the devel version, see CellMixS.

Evaluate Cellspecific Mixing

Bioconductor version: Release (3.20)

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.lue at gmail.com>

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

Installation

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


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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, GeneExpression, SingleCell, Software, Transcriptomics
Version	1.22.0
In Bioconductor since	BioC 3.9 (R-3.6) (5.5 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
System Requirements
URL	https://github.com/almutlue/CellMixS
Bug Reports	https://github.com/almutlue/CellMixS/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
Linking To
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	CellMixS_1.22.0.tar.gz
Windows Binary (x86_64)	CellMixS_1.22.0.zip
macOS Binary (x86_64)	CellMixS_1.22.0.tgz
macOS Binary (arm64)	CellMixS_1.22.0.tgz
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