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phemd

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 gmail.com>

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

Installation

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.

Documentation

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

Details

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
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Package Archives

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

Source Package phemd_1.18.0.tar.gz
Windows Binary phemd_1.18.0.zip
macOS Binary (x86_64) phemd_1.18.0.tgz
macOS Binary (arm64) phemd_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/phemd
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phemd
Bioc Package Browser https://code.bioconductor.org/browse/phemd/
Package Short Url https://bioconductor.org/packages/phemd/
Package Downloads Report Download Stats