Pipeline for augmented co-expression analysis

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Documentation for package ‘GWENA’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.check_data_expr	Run checks on an object to test if it's a data_expr
.check_gost	Run checks on an object to test if it's a gost result
.check_module	Run checks on an object to test if it's a module or a list of modules
.check_network	Run checks on an object to test if it's a network
.contingencyTable	Calculate a contigency table of module overlap between datasets
.cor_func_match	Match a correlation function based on a name
associate_phenotype	Modules phenotpic association
bio_enrich	Modules enrichment
build_graph_from_sq_mat	Return graph from squared matrix network
build_net	Network building by co-expression score computation
compare_conditions	Compare modules topology between conditions
detect_modules	Modules detection in a network
filter_low_var	Filtering genes with low variability
filter_RNA_seq	Filtering of low counts
get_fit.cor	Calculating best fit of a power low on correlation matrix computed on expression data
get_fit.expr	Calculating best fit of a power low on expression data
get_hub_degree	Determine hub genes based on degree
get_hub_genes	Determine hub genes inside each module
get_hub_high_co	Determine hub genes based on connectivity
get_hub_kleinberg	Determine hub genes based on Kleinberg's score
get_sub_clusters	Detect sub clusters
gg_palette	Mimicking ggplot palette Source : https://stackoverflow.com/questions/8197559/emulate-ggplot2-default-color-palette
gtex_expr	Transcriptomic muscle data from GTEx consorsium RNA-seq data
gtex_traits	Traits data linked to samples in transcriptomic data from GTEx
is_data_expr	Determine if an object is a data_expr in sens of GWENA
is_gost	Determine if an object is a gost object
is_module	Determine if an object is a module or a list of modules
is_network	Determine if an object is a network
join_gost	Join gprofiler2::gost results
kuehne_expr	Transcriptomic data from the Kuehne et al. publication
kuehne_traits	Traits data linked to samples in transcriptomic data from the Kuehne et al. publication
plot_comparison_stats	Heatmap of comparison statistics
plot_enrichment	Plot module from bio_enrich
plot_expression_profiles	Modules expression profiles
plot_module	Plot co-expression network
plot_modules_merge	Modules merge plot
plot_modules_phenotype	Heatmap of modules phenotpic association
quiet	Muting a function
z_summary	Calculating Z summary