Package: ClusterGVis 0.1.2

ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data

Streamlining the clustering and visualization of time-series gene expression data from RNA-Seq experiments, this tool supports fuzzy c-means and k-means clustering algorithms. It is compatible with outputs from widely-used packages such as 'Seurat', 'Monocle', and 'WGCNA', enabling seamless downstream visualization and analysis. See Lokesh Kumar and Matthias E Futschik (2007) <doi:10.6026/97320630002005> for more details.

Authors:Jun Zhang [aut, cre]

ClusterGVis_0.1.2.tar.gz
ClusterGVis_0.1.2.zip(r-4.5)ClusterGVis_0.1.2.zip(r-4.4)
ClusterGVis_0.1.2.tgz(r-4.5-any)ClusterGVis_0.1.2.tgz(r-4.4-any)
ClusterGVis_0.1.2.tar.gz(r-4.5-noble)ClusterGVis_0.1.2.tar.gz(r-4.4-noble)
ClusterGVis_0.1.2.tgz(r-4.4-emscripten)
ClusterGVis.pdf |ClusterGVis.html✨
ClusterGVis/json (API)

# Install 'ClusterGVis' in R:

install.packages('ClusterGVis', repos = c('https://junjunlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/junjunlab/clustergvis/issues

Datasets:

BEAM_res - This is a test data for this package test data describtion
exps - This is a test data for this package test data describtion
net - This is a test data for this package test data describtion
sig_gene_names - This is a test data for this package test data describtion
termanno - This is a test data for this package test data describtion
termanno2 - This is a test data for this package test data describtion

On CRAN:

sequencing clusterprofiler summarizedexperiment mfuzz complexheatmap gene-clustering gene-expression visualization

6.80 score 281 stars 30 scripts 657 downloads 14 exports 212 dependencies

Last updated 7 days agofrom:3f091f563f. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 10 2025
R-4.5-win	NOTE	Mar 10 2025
R-4.5-mac	NOTE	Mar 10 2025
R-4.5-linux	NOTE	Mar 10 2025
R-4.4-win	NOTE	Mar 10 2025
R-4.4-mac	NOTE	Mar 10 2025
R-4.4-linux	NOTE	Mar 10 2025

Exports:%>%clusterData enrichCluster exprs getClusters normalized_counts plot_genes_branched_heatmap2 plot_multiple_branches_heatmap2 plot_pseudotime_heatmap2 pre_pseudotime_matrix prepareDataFromscRNA pseudotime size_factors visCluster

Dependencies:abind AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot broom bslib cachem car carData circlize class cli clue cluster clusterProfiler codetools colorRamps colorspace ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray dendextend Deriv digest doBy doParallel DOSE dplyr DT DynDoc e1071 edgeR ellipse emmeans enrichplot estimability evaluate factoextra FactoMineR fansi farver fastmap fastmatch fgsea flashClust fontawesome foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges GetoptLong ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtangle ggtree GlobalOptions glue GO.db GOSemSim gridExtra gridGraphics gson gtable highr htmltools htmlwidgets httpuv httr igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise Mfuzz mgcv microbenchmark mime minqa modelr multcompView munsell mvtnorm nlme nloptr nnet numDeriv openssl patchwork pbkrtest pillar pkgconfig plogr plyr png polyclip polynom promises proxy purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas reshape2 Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rstatix S4Arrays S4Vectors sass scales scatterpie scatterplot3d shape SingleCellExperiment snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts TCseq tibble tidyr tidyselect tidytree tinytex tkWidgets treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite widgetTools withr xfun XVector yaml yulab.utils

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
This is a test data for this package test data describtion	BEAM_res
Cluster Data Based on Different Methods	clusterData
Perform GO/KEGG Enrichment Analysis for Multiple Clusters	enrichCluster
Generic to access cds count matrix	exprs
Method to access cds count matrix	exprs,cell_data_set-method
This is a test data for this package test data describtion	exps
using filter.std to filter low expression genes	filter.std filter.std modified by Mfuzz filter.std
Determine Optimal Clusters for Gene Expression or Pseudotime Data	getClusters
This is a test data for this package test data describtion	net
Return a size-factor normalized and (optionally) log-transformed expression	normalized_counts
Create a heatmap to demonstrate the bifurcation of gene expression along two branchs which is slightly modified in monocle2	plot_genes_branched_heatmap2
Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches	plot_multiple_branches_heatmap2
Plots a pseudotime-ordered, row-centered heatmap which is slightly modified in monocle2	plot_pseudotime_heatmap2
Calculate and return a smoothed pseudotime matrix for the given gene list	pre_pseudotime_matrix
Prepare scRNA Data for clusterGvis Analysis	prepareDataFromscRNA
Generic to extract pseudotime from CDS object	pseudotime
Method to extract pseudotime from CDS object	pseudotime,cell_data_set-method
This is a test data for this package test data describtion	sig_gene_names
Get the size factors from a cds object.	size_factors
This is a test data for this package test data describtion	termanno
This is a test data for this package test data describtion	termanno2
traverseTree function	traverseTree
using visCluster to visualize cluster results from clusterData and enrichCluster output	visCluster