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cytoMEM

Marker Enrichment Modeling (MEM)


Bioconductor version: Release (3.18)

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] , Kirsten Diggins [aut] , Jonathan Irish [aut, cre]

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

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

Installation

To install this package, start R (version "4.3") and enter:


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

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

Details

biocViews CellBiology, Classification, Clustering, DataImport, DataRepresentation, FlowCytometry, Proteomics, SingleCell, Software, SystemsBiology
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package cytoMEM_1.6.0.tar.gz
Windows Binary cytoMEM_1.6.0.zip
macOS Binary (x86_64) cytoMEM_1.6.0.tgz
macOS Binary (arm64) cytoMEM_1.6.0.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