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ClusterFoldSimilarity

This is the development version of ClusterFoldSimilarity; to use it, please install the devel version of Bioconductor.

Calculate similarity of clusters from different single cell samples using foldchanges


Bioconductor version: Development (3.19)

This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m

Author: Oscar Gonzalez-Velasco [cre, aut]

Maintainer: Oscar Gonzalez-Velasco <oscargvelasco at gmail.com>

Citation (from within R, enter citation("ClusterFoldSimilarity")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ClusterFoldSimilarity")

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("ClusterFoldSimilarity")
ClusterFoldSimilarity: HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Clustering, FeatureExtraction, GeneTarget, GraphAndNetwork, RNASeq, SingleCell, Software
Version 0.99.14
In Bioconductor since BioC 3.19 (R-4.4)
License Artistic-2.0
Depends
Imports methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro
System Requirements
URL
See More
Suggests knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
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Package Archives

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

Source Package ClusterFoldSimilarity_0.99.14.tar.gz
Windows Binary ClusterFoldSimilarity_0.99.14.zip
macOS Binary (x86_64) ClusterFoldSimilarity_0.99.14.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/ClusterFoldSimilarity
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ClusterFoldSimilarity
Bioc Package Browser https://code.bioconductor.org/browse/ClusterFoldSimilarity/
Package Short Url https://bioconductor.org/packages/ClusterFoldSimilarity/
Package Downloads Report Download Stats