DOI: 10.18129/B9.bioc.ctgGEM    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ctgGEM.

Generating Tree Hierarchy Visualizations from Gene Expression Data

Bioconductor version: 3.12

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 and Carrie Minette

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 1.2.0
In Bioconductor since BioC 3.11 (R-4.0) (1 year)
License GPL(>=2)
Depends monocle, SummarizedExperiment
Imports Biobase, BiocGenerics, graphics, grDevices, igraph, methods, utils, sincell, TSCAN, destiny, HSMMSingleCell
Suggests BiocStyle, biomaRt, irlba, knitr, VGAM
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Source Package ctgGEM_1.2.0.tar.gz
Windows Binary ctgGEM_1.2.0.zip
macOS 10.13 (High Sierra) ctgGEM_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ctgGEM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ctgGEM
Package Short Url https://bioconductor.org/packages/ctgGEM/
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