get_collectri: CollecTRI gene regulatory network. Wrapper to access...

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

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).

Description

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).

Usage

get_collectri(
  organism = "human",
  split_complexes = FALSE,
  load_meta = FALSE,
  ...
)

Arguments

organism	Which organism to use. Only human, mouse and rat are available.
split_complexes	Whether to split complexes into subunits. By default complexes are kept as they are.
load_meta	Whether to load meta data for the TF-gene interactions. This is set to false by default.
...	Optional additional arguments, passed to OmniPath import_transcriptional_interactions.

Examples

collectri <- get_collectri(organism='human', split_complexes=FALSE)

saezlab/decoupleR documentation built on June 9, 2025, 1:55 p.m.