I am struggling with running WGCNA on cuffdiff output consisting of 28 pairwise comparisons (Time series Analysis).
Can someone suggest way out to perform WGCNA for each comparisons separately.
What have you tried? - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.
I have used Cuffdiff after STAR.
What have you tried to solve your WGCNA question?
Cross-posted on Bioconductor: https://support.bioconductor.org/p/113105/
The WGCNA developer replied to you on Bioconductor but never followed-up.
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