Package: cytoMEM
Type: Package
Title: Marker Enrichment Modeling (MEM)
Version: 1.6.0
Authors@R: c(person("Sierra","Lima", role = c("aut"),
  		email = "sierrambarone@gmail.com",
  		comment = c(ORCID = "0000-0001-5944-750X")),   
		person("Kirsten","Diggins", role = c("aut"),
  		comment = c(ORCID = "0000-0003-1622-0158")),
		person("Jonathan","Irish", role = c("aut","cre"),
  		email = "jonathan.irish@vanderbilt.edu",
  		comment = c(ORCID = "0000-0001-9428-8866")))
Description: 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.
License: GPL-3
Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats,
        methods
Collate:
        'MEM_function.R''create_labels_txt.R''IQR_thresh.R''build_heatmaps.R''add_cluster_ID.R''add_fileID_to_clusterID.R''choose_reference_pop.R''choose_markers.R''create_labels.R''format_data.R''get_files.R''rename_markers.R''MEM_RMSD.R''zero_reference.R'
biocViews: Proteomics, SystemsBiology, Classification, FlowCytometry,
        DataRepresentation, DataImport, CellBiology, SingleCell,
        Clustering
Depends: R (>= 4.2.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/cytolab/cytoMEM
git_url: https://git.bioconductor.org/packages/cytoMEM
git_branch: RELEASE_3_18
git_last_commit: 0556dc3
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 20:52:39 UTC; biocbuild
Author: Sierra Lima [aut] (<https://orcid.org/0000-0001-5944-750X>),
  Kirsten Diggins [aut] (<https://orcid.org/0000-0003-1622-0158>),
  Jonathan Irish [aut, cre] (<https://orcid.org/0000-0001-9428-8866>)
Maintainer: Jonathan Irish <jonathan.irish@vanderbilt.edu>
Built: R 4.3.2; ; 2023-12-06 14:34:11 UTC; unix
