Man pages for Bioconductor-mirror/CEMiTool
Finds Gene Co-expression Modules

cemCEMiTool Object
cemitoolFull gene co-expression analysis
CEMiTool-classAn S4 class to represent the CEMiTool analysis.
cemoverlapIntegrates CEMiTool analyses
exprYellow Fever gene expression data from GEO study GSE13485
expr_dataRetrieve and set expression attribute
expr_pct_filterFilter genes based on expression.
filter_exprFilter gene expression table
find_modulesCo-expression modules definition
generate_reportCEMiTool report
get_hubsGet hubs
gsea_dataRetrieve Gene Set Enrichment Analysis (GSEA) results
interactions_dataRetrieve and set interaction data to CEMiTool object
mod_colorsRetrieve and set mod_colors attribute
mod_gseaModule Gene Set Enrichment Analysis
mod_oraModule Overrepresentation Analysis
mod_summaryCo-expression module summarization
module_genesGet the module genes in a CEMiTool object
module_namesGet module names in a CEMiTool object
new_cemCreate a CEMiTool object
nmodulesGet the number of modules in a CEMiTool object
ora_dataRetrieve over representation analysis (ORA) results
plot_beta_r2Soft-threshold beta selection graph
plot_gseaGSEA visualization
plot_interactionsNetwork visualization
plot_mean_kNetwork mean connectivity
plot_oraORA visualization
plot_ora_singleORA visualization for one module
plot_profileExpression profile visualization
read_gmtRead a GMT file
sample_annotYellow Fever Sample Annotation data
sample_annotationRetrive or set the sample_annotation attribute
show-CEMiTool-methodPrint a cemitool object
show_plotRetrieve CEMiTool object plots
vstPerform variance stabilizing transformation on expression...
write_filesSave the CEMiTool object in files
Bioconductor-mirror/CEMiTool documentation built on Aug. 8, 2017, 12:37 a.m.