phemd
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see phemd.
Phenotypic EMD for comparison of single-cell samples
Bioconductor version: 3.15
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("phemd")):
Installation
To install this package, start R (version "4.2") 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 |
Details
| 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) (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 |
See More
| Suggests | knitr |
| Linking To | |
| Enhances | |
| 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_1.12.0.tar.gz |
| Windows Binary | phemd_1.12.0.zip |
| macOS Binary (x86_64) | phemd_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/phemd |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/phemd |
| Package Short Url | https://bioconductor.org/packages/phemd/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |