decoupleR - decoupleR: Ensemble of computational methods to infer biological activities from omics data
Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR 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.
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differentialexpressionfunctionalgenomicsgeneexpressiongeneregulationnetworksoftwarestatisticalmethodtranscription
10.46 score 312 stars 7 dependents 874 scripts 3.9k downloadsdorothea - Collection Of Human And Mouse TF Regulons
DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence.
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experimentdatahomo_sapiens_datamus_musculus_databioconductor-packagefunctional-analysisgene-expressionregulonstf-activitiestranscription-factordatapkg
7.82 score 163 stars 454 scripts