Package: CEMiTool 1.37.0

Helder Nakaya

CEMiTool: Co-expression Modules identification Tool

The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

Authors:Pedro Russo [aut], Gustavo Ferreira [aut], Matheus Bürger [aut], Lucas Cardozo [aut], Diogenes Lima [aut], Thiago Hirata [aut], Melissa Lever [aut], Helder Nakaya [aut, cre]

CEMiTool_1.37.0.tar.gz
CEMiTool_1.37.0.zip(r-4.7)CEMiTool_1.37.0.zip(r-4.6)CEMiTool_1.37.0.zip(r-4.5)
CEMiTool_1.37.0.tgz(r-4.6-any)CEMiTool_1.37.0.tgz(r-4.5-any)
CEMiTool_1.37.0.tar.gz(r-4.7-any)CEMiTool_1.37.0.tar.gz(r-4.6-any)
CEMiTool_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CEMiTool/json (API)

# Install 'CEMiTool' in R:

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

Datasets:

cem - CEMiTool Object
expr0 - Yellow Fever gene expression data from GEO study GSE13485
sample_annot - Yellow Fever Sample Annotation data

On BioConductor:CEMiTool-1.37.0(bioc 3.24)CEMiTool-1.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression transcriptomics graphandnetwork mrnamicroarray rnaseq network networkenrichment pathways immunooncology

6.22 score 83 scripts 540 downloads 31 mentions 50 exports 181 dependencies

Last updated from:dffeb392d5. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	252
linux-devel-x86_64	NOTE	406
source / vignettes	OK	425
linux-release-x86_64	NOTE	482
macos-release-arm64	NOTE	294
macos-oldrel-arm64	NOTE	194
windows-devel	NOTE	349
windows-release	NOTE	341
windows-oldrel	NOTE	315
wasm-release	OK	199

Exports:adj_data adj_data<-cemitool diagnostic_report expr_data expr_data<-filter_genes find_modules fit_data generate_report get_adj get_beta_data get_cemitool_r2_beta get_connectivity get_hubs get_merged_mods get_mods get_phi gsea_data interactions_data interactions_data<-mod_colors mod_colors<-mod_gene_num mod_gsea mod_names mod_ora mod_summary module_genes new_cem nmodules ora_data plot_beta_r2 plot_gsea plot_hist plot_interactions plot_mean_k plot_mean_var plot_ora plot_profile plot_qq plot_sample_tree read_gmt sample_annotation sample_annotation<-save_plots select_genes show show_plot write_files

Dependencies:aisdk AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot bslib cachem callr caTools checkmate cli cluster clusterProfiler coda codetools colorspace confintr cowplot cpp11 crayon crosstalk curl data.table DBI digest doParallel DOSE dplyr DT dynamicTreeCut enrichit enrichplot evaluate farver fastcluster fastmap fastmatch fgsea fontawesome fontBitstreamVera fontLiberation fontquiver foreach foreign formatR Formula fs futile.logger futile.options gdtools generics ggdendro ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpmisc ggpp ggrepel ggtangle ggthemes ggtree glue GO.db GOSemSim gridExtra gridGraphics gson gtable highr Hmisc htmlTable htmltools htmlwidgets httr httr2 igraph impute intergraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle lubridate magrittr MASS Matrix MatrixModels matrixStats memoise mime network nlme nnet openssl otel patchwork pillar pkgconfig plyr png polyclip polynom pracma preprocessCore processx promises ps purrr quantreg qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown rpart RSQLite rstudioapi S4Vectors S7 sass scales scatterpie Seqinfo sna snow SparseM splus2R statnet.common stringi stringr survival sys systemfonts tibble tidydr tidyr tidyselect tidytree timechange tinytex treeio tweenr utf8 vctrs viridisLite WGCNA withr xfun xts XVector yaml yulab.utils zoo

CEMiTool: Co-expression Modules Identification Tool

Rendered fromCEMiTool.Rmdusingknitr::rmarkdown

Last update: 2025-10-13
Started: 2017-01-28

Help page	Topics
Get or set adjacency matrix value	adj_data adj_data,CEMiTool-method adj_data<- adj_data<-,CEMiTool-method
CEMiTool Object	cem
Full gene co-expression analysis	cemitool
An S4 class to represent the CEMiTool analysis.	CEMiTool-class
Diagnostic report	diagnostic_report diagnostic_report,CEMiTool-method
Retrieve and set expression attribute	expr_data expr_data,CEMiTool-method expr_data<- expr_data<-,CEMiTool-method
Yellow Fever gene expression data from GEO study GSE13485	expr0
Filter a gene expression data.frame	filter_genes
Co-expression modules definition	find_modules find_modules,CEMiTool-method
Retrieve scale-free model fit data	fit_data fit_data,CEMiTool-method
CEMiTool report	generate_report generate_report,CEMiTool-method
Calculate adjacency matrix	get_adj get_adj,CEMiTool-method
Soft-threshold beta data	get_beta_data get_beta_data,CEMiTool-method
Calculate CEMiTool beta and R2 values	get_cemitool_r2_beta get_cemitool_r2_beta,CEMiTool-method
Calculate network connectivity	get_connectivity get_connectivity,CEMiTool-method
Get hubs	get_hubs get_hubs,CEMiTool-method
Merge similar modules	get_merged_mods get_merged_mods,CEMiTool-method
Calculate co-expression modules	get_mods get_mods,CEMiTool-method
Calculate phi	get_phi get_phi,CEMiTool-method
Retrieve Gene Set Enrichment Analysis (GSEA) results	gsea_data gsea_data,CEMiTool-method
Retrieve and set interaction data to CEMiTool object	interactions_data interactions_data,CEMiTool-method interactions_data<- interactions_data<-,CEMiTool-method
Retrieve and set mod_colors attribute	mod_colors mod_colors,CEMiTool-method mod_colors<- mod_colors<-,CEMiTool,character-method
Get the number of genes in modules in a CEMiTool object	mod_gene_num mod_gene_num,CEMiTool-method
Module Gene Set Enrichment Analysis	mod_gsea mod_gsea,CEMiTool-method
Get module names in a CEMiTool object	mod_names mod_names,CEMiTool-method
Module Overrepresentation Analysis	mod_ora mod_ora,CEMiTool-method
Co-expression module summarization	mod_summary mod_summary,CEMiTool-method
Get the module genes in a CEMiTool object	module_genes module_genes,CEMiTool-method
Create a CEMiTool object	new_cem
Get the number of modules in a CEMiTool object	nmodules nmodules,CEMiTool-method
Retrieve over representation analysis (ORA) results	ora_data ora_data,CEMiTool-method
Soft-threshold beta selection graph	plot_beta_r2 plot_beta_r2,CEMiTool-method
GSEA visualization	plot_gsea plot_gsea,CEMiTool-method
Plot histogram	plot_hist plot_hist,CEMiTool-method
Network visualization	plot_interactions plot_interactions,CEMiTool-method
Network mean connectivity	plot_mean_k plot_mean_k,CEMiTool-method
Plot mean and variance	plot_mean_var plot_mean_var,CEMiTool-method
ORA visualization	plot_ora plot_ora,CEMiTool-method
Expression profile visualization	plot_profile plot_profile,CEMiTool-method
Plot quantile-quantile plot	plot_qq plot_qq,CEMiTool-method
Sample clustering	plot_sample_tree plot_sample_tree,CEMiTool-method
Read a GMT file	read_gmt
Yellow Fever Sample Annotation data	sample_annot
Retrive or set the sample_annotation attribute	sample_annotation sample_annotation,CEMiTool-method sample_annotation<- sample_annotation<-,CEMiTool-method
Save CEMiTool object plots	save_plots save_plots,CEMiTool-method
Select genes based on variance	select_genes
Retrieve CEMiTool object plots	show_plot show_plot,CEMiTool-method
Print a cemitool object	show,CEMiTool-method
Save the CEMiTool object in files	write_files write_files,CEMiTool-method

Package: CEMiTool 1.37.0

CEMiTool: Co-expression Modules identification Tool

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