--- a +++ b/docs/source/pycombatseq.rst @@ -0,0 +1,22 @@ +pycombat_seq: batch effect correction for RNASeq data +===================================================== + +.. currentmodule:: inmoose.pycombat + +ComBat-Seq [Zhang2020]_ follows on the steps of ComBat, but targets specifically +RNA-Seq data. Conceptually, ComBat-Seq is based on the same mathematical +framework as ComBat, except that its replaces the normal distribution of +microarray data by a negative binomial distribution to account for the +specificities of RNA-Seq expression data. :func:`pycombat_seq` is a direct port +of ComBat-Seq to Python. Since ComBat-Seq relies on the Bioconductor +:code:`edgeR` package, the relevant parts of :code:`edgeR` have been ported +along. Closely following the original implementation in R, :func:`pycombat_seq` +has results very similar to those of ComBat-Seq in terms of batch effects +correction. Additionally, :func:`pycombat_seq` is as fast, if not faster, than +the original implementation in R. It also features additional capabilities, such +as fixing a given batch as reference. + +Code documentation +------------------ + +.. autofunction:: pycombat_seq