phemd

DOI: 10.18129/B9.bioc.phemd    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see phemd.

Phenotypic EMD for comparison of single-cell samples

Bioconductor version: 3.13

Package for comparing and generating a low-dimensional embedding of multiple single-cell samples.

Author: William S Chen

Maintainer: William S Chen <wil.yum.chen at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("phemd")

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("phemd")

 

HTML	R Script	PhEMD vignette
PDF		Reference Manual

Details

biocViews	Clustering, ComparativeGenomics, DataRepresentation, DimensionReduction, MultipleComparison, Proteomics, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL-2
Depends	R (>= 3.5), monocle
Imports	SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
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	phemd_1.8.0.tar.gz
Windows Binary	phemd_1.8.0.zip
macOS 10.13 (High Sierra)	phemd_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phemd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/phemd
Package Short Url	https://bioconductor.org/packages/phemd/
Package Downloads Report	Download Stats