CellMixS

DOI: 10.18129/B9.bioc.CellMixS    

Evaluate Cellspecific Mixing

Bioconductor version: Release (3.11)

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 "4.0") 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 1.4.1
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License GPL (>=2)
Depends kSamples, R (>= 3.6)
Imports BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, limma
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_1.4.1.tar.gz
Windows Binary CellMixS_1.4.1.zip
macOS 10.13 (High Sierra) CellMixS_1.4.1.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
Old Source Packages for BioC 3.11 Source Archive

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