ctgGEM
This package is for version 3.11 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: 3.11
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("ctgGEM")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
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) (4 years) |
| License | GPL(>=2) |
| Depends | monocle, SummarizedExperiment |
| Imports | Biobase, BiocGenerics, graphics, grDevices, ggplot2, igraph, Matrix, methods, Matrix, utils, sincell, TSCAN, HSMMSingleCell |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, biomaRt, irlba, knitr, destiny, VGAM |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.11 | Source Archive |