PyDESeq2
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Option to specify control genes for fitting size factors
The original DESeq2 package enables one to specify "control genes" that are used to fit the size factors. These are genes that are not expected to be changing between samples. See: https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/estimateSizeFactors
It would be great if the "deseq2" function and "fit_size_factors" function enabled the user to pass a list of control genes that would be used to estimate the size factors. These genes should be a subset of the genes in the full dataset.