DOI: 10.18129/B9.bioc.phemd    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Phenotypic EMD for comparison of single-cell samples

Bioconductor version: Release (3.15)

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>

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


To install this package, start R (version "4.2") and enter:

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


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


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biocViews Clustering, ComparativeGenomics, DataRepresentation, DimensionReduction, MultipleComparison, Proteomics, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.12.0
In Bioconductor since BioC 3.9 (R-3.6) (3 years)
License GPL-2
Depends R (>= 3.5), 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
Suggests knitr
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