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CellMixS

Evaluate Cellspecific Mixing


Bioconductor version: Release (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")

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 1.18.0
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
System Requirements
URL https://github.com/almutlue/CellMixS
Bug Reports https://github.com/almutlue/CellMixS/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
Linking To
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Build Report Build Report

Package Archives

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

Source Package CellMixS_1.18.0.tar.gz
Windows Binary CellMixS_1.18.0.zip
macOS Binary (x86_64) CellMixS_1.18.0.tgz
macOS Binary (arm64) CellMixS_1.18.0.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