SantosRAC / conekt_grasses_microbiome

MIT License
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Add functions to internally compute correlations (integration) #6

Open SantosRAC opened 1 month ago

SantosRAC commented 1 month ago

Add functions to internally compute correlations between OTU/ASV counts (transformed) and gene expression (transformed). After importing expression profiles and ASV/OTU counts, admins must be able to compute the correlations for pairs of gene - ASV/OTU.

Implementation involves:

SantosRAC commented 1 week ago

UPDATES: for studies that have equal number of runs in the transcriptome and in the microbiome datasets/matrices, currently CORALS is being used to compute Pearson correlations between genes and microbes (OTUs). Adaptations will be made pretty soon to also accommodate correlations with ASVs.