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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | ClusterGVis_1.0.0.tgz |
| 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 |