CellMixS

DOI: 10.18129/B9.bioc.CellMixS    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CellMixS.

Evaluate Cellspecific Mixing

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	BatchEffect, GeneExpression, SingleCell, Software, Transcriptomics
Version	1.6.1
In Bioconductor since	BioC 3.9 (R-3.6) (2 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
SystemRequirements
Enhances
URL	https://github.com/almutlue/CellMixS
BugReports	https://github.com/almutlue/CellMixS/issues
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_1.6.1.tar.gz
Windows Binary	CellMixS_1.6.1.zip
macOS 10.13 (High Sierra)	CellMixS_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CellMixS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CellMixS
Package Short Url	https://bioconductor.org/packages/CellMixS/
Package Downloads Report	Download Stats