Package index • decoupleR

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