DOI: 10.18129/B9.bioc.ctgGEM  

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 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ctgGEM.

Generating Tree Hierarchy Visualizations from Gene Expression Data

Bioconductor version: 3.16

Cell Tree Generator for Gene Expression Matrices (ctgGEM) streamlines the building of cell-state hierarchies from single-cell gene expression data across multiple existing tools for improved comparability and reproducibility. It supports pseudotemporal ordering algorithms and visualization tools from monocle, cellTree, TSCAN, sincell, and destiny, and provides a unified output format for integration with downstream data analysis workflows and Cytoscape.

Author: Mark Block [aut], Carrie Minette [aut], Evgeni Radichev [aut], Etienne Gnimpieba [aut], Mariah Hoffman [aut], USD Biomedical Engineering [aut, cre]

Maintainer: USD Biomedical Engineering <bicbioeng at gmail.com>

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


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biocViews Clustering, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, MultipleComparison, QualityControl, RNASeq, Sequencing, SingleCell, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL(>=2)
Depends monocle, SummarizedExperiment
Imports Biobase, BiocGenerics, graphics, grDevices, igraph, Matrix, methods, utils, sincell, TSCAN
Suggests BiocStyle, biomaRt, HSMMSingleCell, irlba, knitr, rmarkdown, VGAM
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