Registration and Call for Abstracts Open for Bioc2024


Phenotypic EMD for comparison of single-cell samples

Bioconductor version: Release (3.18)

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

Author: William S Chen [aut, cre]

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

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

PhEMD vignette HTML R Script
Reference Manual PDF


biocViews Clustering, ComparativeGenomics, DataRepresentation, DimensionReduction, MultipleComparison, Proteomics, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Depends R (>= 4.0), monocle, Seurat
Imports SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate
System Requirements
See More
Suggests knitr, BiocStyle
Linking To
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 phemd_1.18.0.tar.gz
Windows Binary
macOS Binary (x86_64) phemd_1.18.0.tgz
macOS Binary (arm64) phemd_1.18.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats