CellMixS
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CellMixS.
Evaluate Cellspecific Mixing
Bioconductor version: 3.19
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("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 | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, GeneExpression, SingleCell, Software, Transcriptomics |
| Version | 1.20.0 |
| 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 |
See More
| 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | CellMixS_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | CellMixS_1.20.0.tgz |
| macOS Binary (arm64) | CellMixS_1.20.0.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 |