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Batch Correction in RNA-seq data

Reddit r/bioinformatics·u/Putrid-Raisin-5476·about 1 month ago
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Batch Correction in RNA-seq data Hi everyone, I am working on a Python package for RNA-Seq deconvolution. To correct for the effects of multiple batches in the inputed bulk data, I wanted to use ComBat-Seq, which was originally implemented in R but also has a Python implementation in the inmoose package. The problem with inmoose, however, is that it is licensed under the GPL. I would prefer to release my package under the MIT licence, which would not be possible if I were to import a method from a GPL-licensed package... I have considered using the Combat function from Scanpy, but I am not sure whether Combat is suitable, as it was originally designed for microarray data. Furthermore, Combat is based on the statistical assumption that the data is normally distributed, which is as far as I know not the case with RNA-Seq count data.…

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