CellMixS

Evaluate Cellspecific Mixing

Bioconductor version: 3.23 · Package version: 1.28.0

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.

Installation

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

BiocManager::install("CellMixS")

Details

Maintainer	Almut Lütge <almut.lue@gmail.com>
Author	Almut Lütge [aut, cre]
License	GPL (>=2)
URL	https://github.com/almutlue/CellMixS
Bug Reports	https://github.com/almutlue/CellMixS/issues
Downloads rank	448
Source branch	RELEASE_3_23
biocViews	BatchEffect, GeneExpression, SingleCell, Software, Transcriptomics

Documentation

Explore data integration and batch effects

Download

Source package

Dependencies

Depends: kSamples, R (>= 4.0)

Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics

Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne