ctgGEM

This package is for version 3.14 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: 3.14

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")):

Installation

To install this package, start R (version "4.1") and enter:


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

BiocManager::install("ctgGEM")

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("ctgGEM")
ctgGEM HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, MultipleComparison, QualityControl, RNASeq, Sequencing, SingleCell, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL(>=2)
Depends monocle, SummarizedExperiment
Imports Biobase, BiocGenerics, graphics, grDevices, igraph, Matrix, methods, utils, sincell, TSCAN
System Requirements
URL
See More
Suggests BiocStyle, biomaRt, HSMMSingleCell, irlba, knitr, rmarkdown, VGAM
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Depends On Me
Imports Me
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Package Archives

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

Source Package ctgGEM_1.6.0.tar.gz
Windows Binary ctgGEM_1.6.0.zip
macOS 10.13 (High Sierra) ctgGEM_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ctgGEM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ctgGEM
Bioc Package Browser https://code.bioconductor.org/browse/ctgGEM/
Package Short Url https://bioconductor.org/packages/ctgGEM/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive