phemd

DOI: 10.18129/B9.bioc.phemd    

Phenotypic EMD for comparison of single-cell samples

Bioconductor version: Release (3.9)

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")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script PhEMD vignette
PDF   Reference Manual

Details

biocViews Clustering, ComparativeGenomics, DataRepresentation, DimensionReduction, MultipleComparison, Proteomics, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.0.1
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-2
Depends R (>= 3.6), monocle
Imports SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package phemd_1.0.1.tar.gz
Windows Binary phemd_1.0.1.zip
Mac OS X 10.11 (El Capitan) phemd_1.0.1.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 3.9 Source Archive

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