Man pages for Kumquatum/GWENA
Pipeline for augmented co-expression analysis
| 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 |
| dot-check_data_expr | Run checks on an object to test if it's a data_expr |
| dot-check_gost | Run checks on an object to test if it's a gost result |
| dot-check_module | Run checks on an object to test if it's a module or a list of... |
| dot-check_network | Run checks on an object to test if it's a network |
| dot-contingencyTable | Calculate a contigency table of module overlap between... |
| dot-cor_func_match | Match a correlation function based on a name |
| 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... |
| 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 :... |
| gtex_expr | Transcriptomic muscle data from GTEx consorsium RNA-seq data |
| gtex_traits | Traits data linked to samples in transcriptomic data from... |
| 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... |
| matchsub | Functions from NetRep packages |
| orderAsNumeric | Order the module vector numerically |
| 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 |
