Panpipes: a pipeline for multiomic single-cell data analysis.

Rich-Griffin, C.; Curion, F.; Thomas, T.; Agarwal, D.; Theis, F. J.; Dendrou, C.

doi:10.1101/2023.03.11.532085

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bioRxiv · 10.1101/2023.03.11.532085

Panpipes: a pipeline for multiomic single-cell data analysis.

Rich-Griffin, C.·Curion, F.·Thomas, T.·Agarwal, D.·Theis, F. J.·Dendrou, C.

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Abstract

Single-cell multiomic analysis of the epigenome, transcriptome and proteome allows for comprehensive characterisation of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets presents a challenge given a paucity of approaches for systematic, joint evaluation of different modalities. Here, we present Panpipes, a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.

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Rich-Griffin, C., Curion, F., Thomas, T., Agarwal, D., Theis, F. J., Dendrou, C.. 2023-03-12. Panpipes: a pipeline for multiomic single-cell data analysis.. https://doi.org/10.1101/2023.03.11.532085

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