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decoupleR

decouple()
Evaluate multiple statistics with same input data

Statistics

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)

Network converters

convert_f_defaults()
Rename columns and add defaults values if column not present
rename_net()
Rename network
extract_sets()
Extract sets

Utils

check_corr()
Check correlation (colinearity)
get_toy_data()
Generate a toy mat and network.
show_methods()
Show methods
.fit_preprocessing()
Pre-processing for methods that fit networks.
filt_minsize()
Filter sources with minsize targets
intersect_regulons()
Intersect network target features with input matrix.

Omnipath wrappers

show_resources()
Shows available resources in Omnipath. For more information visit the official website for Omnipath.
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_dorothea()
DoRothEA gene regulatory network.
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_progeny()
Pathway RespOnsive GENes for activity inference (PROGENy).
get_ksn_omnipath()
OmniPath kinase-substrate network