.fit_preprocessing |
Pre-processing for methods that fit networks. |
check_corr |
Check correlation (colinearity) |
convert_f_defaults |
Rename columns and add defaults values if column not present |
decouple |
Evaluate multiple statistics with same input data |
extract_sets |
Extract sets |
filt_minsize |
Filter sources with minsize targets |
get_collectri |
CollecTRI gene regulatory network. Wrapper to access CollecTRI gene regulatory network. CollecTRI is a comprehensive resource containing a curated collection of transcription factors (TFs) and their target genes. It is an expansion of DoRothEA. Each interaction is weighted by its mode of regulation (either positive or negative). |
get_dorothea |
DoRothEA gene regulatory network. |
get_ksn_omnipath |
OmniPath kinase-substrate network |
get_progeny |
Pathway RespOnsive GENes for activity inference (PROGENy). |
get_resource |
Wrapper to access resources inside Omnipath. This wrapper allows to easily query different prior knowledge resources. To check available resources run 'decoupleR::show_resources()'. For more information visit the official website for Omnipath. |
get_toy_data |
Generate a toy 'mat' and 'network'. |
intersect_regulons |
Intersect network target features with input matrix. |
rename_net |
Rename network |
run_aucell |
AUCell |
run_consensus |
Consensus score between methods |
run_fgsea |
Fast Gene Set Enrichment Analysis (FGSEA) |
run_gsva |
Gene Set Variation Analysis (GSVA) |
run_mdt |
Multivariate Decision Trees (MDT) |
run_mlm |
Multivariate Linear Model (MLM) |
run_ora |
Over Representation Analysis (ORA) |
run_udt |
Univariate Decision Tree (UDT) |
run_ulm |
Univariate Linear Model (ULM) |
run_viper |
Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER) |
run_wmean |
Weighted Mean (WMEAN) |
run_wsum |
Weighted Sum (WSUM) |
show_methods |
Show methods |
show_resources |
Shows available resources in Omnipath. For more information visit the official website for Omnipath. |