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

## Documentation for package ‘decoupleR’ version 2.12.0

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

## Help Pages

.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.