cytoMEM

This is the development version of cytoMEM; for the stable release version, see cytoMEM.

Marker Enrichment Modeling (MEM)

Bioconductor version: Development (3.21)

MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD.

Author: Sierra Lima [aut] (ORCID: ), Kirsten Diggins [aut] (ORCID: ), Jonathan Irish [aut, cre] (ORCID: )

Maintainer: Jonathan Irish <jonathan.irish at vanderbilt.edu>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cytoMEM")

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("cytoMEM")

Intro_to_Marker_Enrichment_Modeling_Analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBiology, Classification, Clustering, DataImport, DataRepresentation, FlowCytometry, Proteomics, SingleCell, Software, SystemsBiology
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods
System Requirements
URL	https://github.com/cytolab/cytoMEM

Suggests	knitr, rmarkdown
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	cytoMEM_1.11.0.tar.gz
Windows Binary (x86_64)	cytoMEM_1.11.0.zip (64-bit only)
macOS Binary (x86_64)	cytoMEM_1.11.0.tgz
macOS Binary (arm64)	cytoMEM_1.11.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cytoMEM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cytoMEM
Bioc Package Browser	https://code.bioconductor.org/browse/cytoMEM/
Package Short Url	https://bioconductor.org/packages/cytoMEM/
Package Downloads Report	Download Stats