ctgGEM

DOI: 10.18129/B9.bioc.ctgGEM    

Generating Tree Hierarchy Visualizations from Gene Expression Data

Bioconductor version: Release (3.11)

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, Carrie Minette, Evgeni Radichev, Etienne Gnimpieba, Mariah Hoffman

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

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script ctgGEM
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, MultipleComparison, QualityControl, RNASeq, Sequencing, SingleCell, Software, Visualization
Version 1.0.3
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License GPL(>=2)
Depends monocle, SummarizedExperiment
Imports Biobase, BiocGenerics, graphics, grDevices, ggplot2, igraph, Matrix, methods, Matrix, utils, sincell, TSCAN, HSMMSingleCell
LinkingTo
Suggests BiocStyle, biomaRt, irlba, knitr, destiny, VGAM
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ctgGEM_1.0.3.tar.gz
Windows Binary ctgGEM_1.0.3.zip
macOS 10.13 (High Sierra) ctgGEM_1.0.3.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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