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

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end ]

mat:file

Path to the matrix file (e.g. gene/protein expression, etc.). Should be in in tab-separated format (\*.tab)

*.tsv

net:file

The prior knowledge network linking the features of the expression matrix to a process/component (e.g. gene set, transcription factor, kinase, etc.)

*.tsv

Output

name:type
description
pattern

dc_estimate

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end ]

*estimate__decoupler.tsv:file

The file containing the estimation results of the enrichment(s)

*estimate__decoupler.tsv

dc_pvals

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end ]

*pvals__decoupler.tsv:file

The file containing the p-value associated to the estimation results of the enrichment(s)

*pvals__decoupler.tsv

s:file

The file containing the p-value associated to the estimation results of the enrichment(s)

*pvals__decoupler.tsv

versions

versions.yml:file

File containing software versions

versions.yml