phemd

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see phemd.

Phenotypic EMD for comparison of single-cell samples

Bioconductor version: 3.17

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 gmail.com>

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

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


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

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:

browseVignettes("phemd")

PhEMD vignette HTML R Script

Reference Manual PDF

Version 1.16.0

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

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Suggests knitr

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

Source Package phemd_1.16.0.tar.gz

Windows Binary phemd_1.16.0.zip

macOS Binary (x86_64) phemd_1.16.0.tgz

macOS Binary (arm64) phemd_1.16.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/phemd

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phemd

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Old Source Packages for BioC 3.17 Source Archive