ClusterFoldSimilarity
This is the development version of ClusterFoldSimilarity; for the stable release version, see ClusterFoldSimilarity.
Calculate similarity of clusters from different single cell samples using foldchanges
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Oscar Gonzalez-Velasco <oscargvelasco at gmail.com>
citation("ClusterFoldSimilarity")):
Installation
To install this package, start R (version "4.5") 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 | ||
| LICENSE | Text |
Details
| biocViews | Clustering, FeatureExtraction, GeneTarget, GraphAndNetwork, RNASeq, SingleCell, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ClusterFoldSimilarity_1.3.0.tar.gz |
| Windows Binary (x86_64) | ClusterFoldSimilarity_1.3.0.zip |
| macOS Binary (x86_64) | ClusterFoldSimilarity_1.3.0.tgz |
| macOS Binary (arm64) | ClusterFoldSimilarity_1.3.0.tgz |
| 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 |