pydeseq2.preprocessing

Functions

deseq2_norm(counts)

Return normalized counts and size_factors.

pydeseq2.preprocessing.deseq2_norm(counts)

Return normalized counts and size_factors.

Uses the median of ratios method.

Parameters

counts (pandas.DataFrame) – Raw counts. One column per gene, rows are indexed by sample barcodes.

Returns

• deseq2_counts (pandas.DataFrame) – DESeq2 normalized counts. One column per gene, rows are indexed by sample barcodes.

• size_factors (pandas.DataFrame) – DESeq2 normalization factors.