decoupleR: Ensemble of computational methods to infer biological activities from omics data


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Documentation for package ‘decoupleR’ version 2.12.0

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.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.