Integration of large, complex single-cell datasets with Harmony2

bioRxiv (Cold Spring Harbor Laboratory) 2026 Preprint Open access

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Authors: Nikolaos Patikas, Hongcheng Yao, Roopa Madhu, Soumya Raychaudhuri, Martin Hemberg, Ilya Korsunsky
DOI: 10.64898/2026.03.16.711825
Cited by: 5
References: 23

Abstract

Integrating single cell RNA-seq profiles is posing new challenges as datasets are rapidly expanding, now with over 100 million cells in the public domain. We present the latest version of the Harmony integration software, which efficiently scales to >100M cells and >1K datasets without specialized hardware. Moreover, optimizations to the underlying algorithm help prevent overintegration in biologically heterogeneous datasets. Harmony2 enables efficient, accurate integration of large, complex single-cell atlases.

Fields of Study & Subjects

Single-cell and spatial transcriptomics Cell Image Analysis Techniques Domain Adaptation and Few-Shot Learning

Publication details

Journal / source
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Publication date
18 March 2026
Language
EN
Document type
Preprint