Package: CEMiTool 1.31.0

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_1.31.0.tar.gz
CEMiTool_1.31.0.zip(r-4.5)CEMiTool_1.31.0.zip(r-4.4)CEMiTool_1.31.0.zip(r-4.3)
CEMiTool_1.31.0.tgz(r-4.4-any)CEMiTool_1.31.0.tgz(r-4.3-any)
CEMiTool_1.31.0.tar.gz(r-4.5-noble)CEMiTool_1.31.0.tar.gz(r-4.4-noble)
CEMiTool_1.31.0.tgz(r-4.4-emscripten)CEMiTool_1.31.0.tgz(r-4.3-emscripten)
CEMiTool.pdf |CEMiTool.html✨
CEMiTool/json (API)

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

Peer review:

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

On BioConductor:CEMiTool-1.31.0(bioc 3.21)CEMiTool-1.30.0(bioc 3.20)

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

geneexpressiontranscriptomicsgraphandnetworkmrnamicroarrayrnaseqnetworknetworkenrichmentpathwaysimmunooncology

5.79 score 41 scripts 320 downloads 31 mentions 50 exports 183 dependencies

Last updated 2 months agofrom:3dd973517d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:adj_dataadj_data<-cemitooldiagnostic_reportexpr_dataexpr_data<-filter_genesfind_modulesfit_datagenerate_reportget_adjget_beta_dataget_cemitool_r2_betaget_connectivityget_hubsget_merged_modsget_modsget_phigsea_datainteractions_datainteractions_data<-mod_colorsmod_colors<-mod_gene_nummod_gseamod_namesmod_oramod_summarymodule_genesnew_cemnmodulesora_dataplot_beta_r2plot_gseaplot_histplot_interactionsplot_mean_kplot_mean_varplot_oraplot_profileplot_qqplot_sample_treeread_gmtsample_annotationsample_annotation<-save_plotsselect_genesshowshow_plotwrite_files

Dependencies:AnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbootbslibcachemcheckmatecliclusterclusterProfilercodacodetoolscolorspaceconfintrcowplotcpp11crayoncrosstalkcurldata.tableDBIdigestdoParallelDOSEdplyrDTdynamicTreeCutenrichplotevaluatefansifarverfastclusterfastmapfastmatchfgseafontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggdendroggforceggfunggnewscaleggplot2ggplotifyggpmiscggppggrepelggtangleggthemesggtreeglueGO.dbGOSemSimgridExtragridGraphicsgsongtablehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphimputeintergraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelmodel2lubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimemultcompmultcompViewmunsellmvtnormnetworknlmennetopensslpatchworkpillarpkgconfigplogrplyrpngpolyclippolynompracmapreprocessCorepromisespurrrquantregqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrpartRSQLiterstudioapiS4VectorssandwichsassscalesscatterpiesnasnowSparseMsplus2Rstatnet.commonstringistringrsurvivalsyssystemfontsTH.datatibbletidyrtidyselecttidytreetimechangetinytextreeiotweenrUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunxtsXVectoryamlyulab.utilszlibbioczoo

CEMiTool: Co-expression Modules Identification Tool

Rendered fromCEMiTool.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2019-01-14
Started: 2017-01-28

Readme and manuals

Help Manual

Help pageTopics
Get or set adjacency matrix valueadj_data adj_data,CEMiTool-method adj_data<- adj_data<-,CEMiTool-method
CEMiTool Objectcem
Full gene co-expression analysiscemitool
An S4 class to represent the CEMiTool analysis.CEMiTool-class
Diagnostic reportdiagnostic_report diagnostic_report,CEMiTool-method
Retrieve and set expression attributeexpr_data expr_data,CEMiTool-method expr_data<- expr_data<-,CEMiTool-method
Yellow Fever gene expression data from GEO study GSE13485expr0
Filter a gene expression data.framefilter_genes
Co-expression modules definitionfind_modules find_modules,CEMiTool-method
Retrieve scale-free model fit datafit_data fit_data,CEMiTool-method
CEMiTool reportgenerate_report generate_report,CEMiTool-method
Calculate adjacency matrixget_adj get_adj,CEMiTool-method
Soft-threshold beta dataget_beta_data get_beta_data,CEMiTool-method
Calculate CEMiTool beta and R2 valuesget_cemitool_r2_beta get_cemitool_r2_beta,CEMiTool-method
Calculate network connectivityget_connectivity get_connectivity,CEMiTool-method
Get hubsget_hubs get_hubs,CEMiTool-method
Merge similar modulesget_merged_mods get_merged_mods,CEMiTool-method
Calculate co-expression modulesget_mods get_mods,CEMiTool-method
Calculate phiget_phi get_phi,CEMiTool-method
Retrieve Gene Set Enrichment Analysis (GSEA) resultsgsea_data gsea_data,CEMiTool-method
Retrieve and set interaction data to CEMiTool objectinteractions_data interactions_data,CEMiTool-method interactions_data<- interactions_data<-,CEMiTool-method
Retrieve and set mod_colors attributemod_colors mod_colors,CEMiTool-method mod_colors<- mod_colors<-,CEMiTool,character-method
Get the number of genes in modules in a CEMiTool objectmod_gene_num mod_gene_num,CEMiTool-method
Module Gene Set Enrichment Analysismod_gsea mod_gsea,CEMiTool-method
Get module names in a CEMiTool objectmod_names mod_names,CEMiTool-method
Module Overrepresentation Analysismod_ora mod_ora,CEMiTool-method
Co-expression module summarizationmod_summary mod_summary,CEMiTool-method
Get the module genes in a CEMiTool objectmodule_genes module_genes,CEMiTool-method
Create a CEMiTool objectnew_cem
Get the number of modules in a CEMiTool objectnmodules nmodules,CEMiTool-method
Retrieve over representation analysis (ORA) resultsora_data ora_data,CEMiTool-method
Soft-threshold beta selection graphplot_beta_r2 plot_beta_r2,CEMiTool-method
GSEA visualizationplot_gsea plot_gsea,CEMiTool-method
Plot histogramplot_hist plot_hist,CEMiTool-method
Network visualizationplot_interactions plot_interactions,CEMiTool-method
Network mean connectivityplot_mean_k plot_mean_k,CEMiTool-method
Plot mean and varianceplot_mean_var plot_mean_var,CEMiTool-method
ORA visualizationplot_ora plot_ora,CEMiTool-method
Expression profile visualizationplot_profile plot_profile,CEMiTool-method
Plot quantile-quantile plotplot_qq plot_qq,CEMiTool-method
Sample clusteringplot_sample_tree plot_sample_tree,CEMiTool-method
Read a GMT fileread_gmt
Yellow Fever Sample Annotation datasample_annot
Retrive or set the sample_annotation attributesample_annotation sample_annotation,CEMiTool-method sample_annotation<- sample_annotation<-,CEMiTool-method
Save CEMiTool object plotssave_plots save_plots,CEMiTool-method
Select genes based on varianceselect_genes
Retrieve CEMiTool object plotsshow_plot show_plot,CEMiTool-method
Print a cemitool objectshow,CEMiTool-method
Save the CEMiTool object in fileswrite_files write_files,CEMiTool-method