XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data

Authors

Natarajan, S., Sterling, C., Choudhary, N., Khatun, N., Brieske, M.-S., Busch, H. E., Pucker, B.

Abstract

Rapid developments in sequencing technologies have reduced the costs of transcriptomic experiments and resulted in a plethora of publicly available RNA-seq datasets. This is a valuable resource that can be harnessed to obtain novel biological insights through data upcycling. In this wake, we introduce XpBrew, an end-to-end Python workflow that was applied to generate PanXpresso, a comprehensive collection of gene expression datasets covering the taxonomic breadth of plants, animals, fungi, bacteria and archaea. XpBrew (https://github.com/PuckerLab/XpBrew) and PanXpresso (https://doi.org/10.60507/FK2/OBIGQH) are freely available.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 03 Sep 2026.

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