phemd

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see phemd.

Phenotypic EMD for comparison of single-cell samples

Bioconductor version: 3.14

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>

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

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

biocViews	Clustering, ComparativeGenomics, DataRepresentation, DimensionReduction, MultipleComparison, Proteomics, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.10.0
In Bioconductor since	BioC 3.9 (R-3.6) (5 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
System Requirements
URL

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

Source Package	phemd_1.10.0.tar.gz
Windows Binary	phemd_1.10.0.zip
macOS 10.13 (High Sierra)	phemd_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phemd
Source Repository (Developer Access)	git clone [email protected]:packages/phemd
Bioc Package Browser	https://code.bioconductor.org/browse/phemd/
Package Short Url	https://bioconductor.org/packages/phemd/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive