.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.
