Man pages for csbl-usp/CEMiTool
Co-expression Modules identification Tool

adj_dataGet or set adjacency matrix value
cemCEMiTool Object
cemitoolFull gene co-expression analysis
CEMiTool-classAn S4 class to represent the CEMiTool analysis.
cem_overlapIntegrates CEMiTool analyses
diagnostic_reportDiagnostic report
enrich_modsEnriches communities
expr0Yellow 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
fit_dataRetrieve scale-free model fit data
generate_reportCEMiTool report
get_adjCalculate adjacency matrix
get_beta_dataSoft-threshold beta data
get_cemitool_r2_betaCalculate CEMiTool beta and R2 values
get_connectivityCalculate network connectivity
get_hubsGet hubs
get_merged_modsMerge similar modules
get_modsCalculate co-expression modules
get_phiCalculate phi
gsea_dataRetrieve Gene Set Enrichment Analysis (GSEA) results
interactions_dataRetrieve and set interaction data to CEMiTool object
makeContMatrixMake a LIMMA contrast matrix
makeLimmaCompMake LIMMA comparisons
mod_activity# Determine module activity based on limma
mod_colorsRetrieve and set mod_colors attribute
mod_compareOverlap statistics
mod_gseaModule Gene Set Enrichment Analysis
mod_infoCompute node information and study information
mod_namesGet module names in a CEMiTool object
mod_oraModule Overrepresentation Analysis
mod_summaryCo-expression module summarization
module_genesGet the module genes in a CEMiTool object
module_to_gmtTransform module genes list to a gmt file
new_cemCreate a CEMiTool object
nmodulesGet the number of modules in a CEMiTool object
ora_dataRetrieve over representation analysis (ORA) results
outer_join_mergeCalculate full outer join for two ffdf objects
overlap_communityGenerates communities from edgelist
plot_beta_r2Soft-threshold beta selection graph
plot_comembershipPlot module edge co-membership
plot_consensusPlot graph of consensus modules
plot_gseaGSEA visualization
plot_histPlot histogram
plot_interactionsNetwork visualization
plot_mean_kNetwork mean connectivity
plot_mean_varPlot mean and variance
plot_oraORA visualization
plot_ora_singleORA visualization for one module
plot_profileExpression profile visualization
plot_qqPlot quantile-quantile plot
plot_sample_treeSample clustering
plot_similarityPlot study module similarity
read_gmtRead a GMT file
sample_annotYellow Fever Sample Annotation data
sample_annotationRetrive or set the sample_annotation attribute
save_plotsSave CEMiTool object plots
show-CEMiTool-methodPrint a cemitool object
show_plotRetrieve CEMiTool object plots
stat_overlap_modsCalculate module overlap statistics
vstPerform variance stabilizing transformation on expression...
write_filesSave the CEMiTool object in files
csbl-usp/CEMiTool documentation built on Dec. 8, 2018, 3:26 p.m.