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("ctgGEM")):
Installation
To install this package, start R (version "4.2") 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
| Reference Manual |
Details
| 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) (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 |
| 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 | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 3.16 | Source Archive |