ClusterGVis
This is the released version of ClusterGVis; for the devel version, see ClusterGVis.
One-Step to Cluster and Visualize Gene Expression Data
Bioconductor version: Release (3.23)
Provides a streamlined workflow for clustering and visualizing gene expression patterns, particularly from time-series RNA-Seq and single-cell experiments. The package is designed to integrate seamlessly within the Bioconductor ecosystem by operating directly on standard data classes such as `SummarizedExperiment` and `SingleCellExperiment`. It implements common clustering algorithms (e.g., k-means, fuzzy c-means) and generates a suite of publication-ready visualizations to explore co-expressed gene modules. Functions are also included to facilitate the visualization of clustering results derived from other popular tools.
Author: Jun Zhang [aut, cre, cph]
Maintainer: Jun Zhang <1138976957 at qq.com>
citation("ClusterGVis")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ClusterGVis")
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("ClusterGVis")| vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5) |
| Imports | colorRamps, dplyr, e1071, factoextra, ggplot2, grDevices, grid, Matrix, methods, purrr, reshape2, scales, stats, tibble, SingleCellExperiment, SummarizedExperiment, igraph, VGAM, scuttle |
| System Requirements | |
| URL | https://github.com/junjunlab/ClusterGVis/ https://junjunlab.github.io/ClusterGvis-manual/ |
| Bug Reports | https://github.com/junjunlab/ClusterGVis/issues |
See More
| Suggests | Biobase, ComplexHeatmap, clusterProfiler, TCseq, org.Mm.eg.db, circlize, knitr, monocle, pheatmap, rmarkdown, Seurat, WGCNA, utils, BiocManager, S4Vectors, pheatmap, testthat (>= 3.0.0) |
| 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 | ClusterGVis_1.0.0.tar.gz |
| Windows Binary (x86_64) | ClusterGVis_0.99.9.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | ClusterGVis_0.99.9.tgz |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | ClusterGVis_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ClusterGVis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ClusterGVis |
| Bioc Package Browser | https://code.bioconductor.org/browse/ClusterGVis/ |
| Package Short Url | https://bioconductor.org/packages/ClusterGVis/ |
| Package Downloads Report | Download Stats |