modules/decoupler_decoupler
decoupler is a package containing different statistical methods to extract biological activities from omics data within a unified framework. It allows to flexibly test any enrichment method with any prior knowledge resource and incorporates methods that take into account the sign and weight. It can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.
Description
decoupler is a package containing different statistical methods to extract biological activities from omics data within a unified framework. It allows to flexibly test any enrichment method with any prior knowledge resource and incorporates methods that take into account the sign and weight. It can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.
Input
Path to the matrix file (e.g. gene/protein expression, etc.).
Should be in in tab-separated format (\*.tab)
*.tsv The prior knowledge network linking the features of the
expression matrix to a process/component (e.g. gene set,
transcription factor, kinase, etc.)
*.tsv Keyword arguments passed to decoupler.decouple() (see
documentation for more information here:
https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.decouple.html#decoupler.decouple).
Arguments specific for a method must be specified with
the method name as a prefix e.g. 'gsea_batch_size'
{arg: val, ..., method_arg: val} maintainers
