normpatch

normpatch

Patch the bias. Keep the biology.

normpatch is an R package for estimating normalization factors from bulk RNA-seq count data. It implements methods based on the DEGES framework, the DEG elimination strategy, which iteratively reduces the influence of DEGs when estimating sample-specific scaling factors (Kadota et al. 2012; Sun et al. 2013). The framework is intended for datasets affected by compositional imbalance or strongly asymmetric DEG patterns, where standard normalization assumptions may not hold.

normpatch is a lightweight successor to the normalization components of the TCC package (Sun et al. 2013). Whereas TCC provides an integrated workflow for normalization and DEG analysis, normpatch focuses on normalization factor estimation and delegates downstream DEG testing to established tools such as edgeR (Chen et al. 2025) and DESeq2 (Love et al. 2014). This narrower scope provides a smaller, more transparent, and more interoperable interface.