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Attribute
Single-Cell & Spatial Biology

Harmony

Broad Institute / Harvard Medical School (Raychaudhuri Lab)
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CategorySingle-Cell & Spatial Biology
CompanyBroad Institute / Harvard Medical School (Raychaudhuri Lab)
PriceFree Open Source
StatusStatus not confirmed
AvailabilityAvailable on CRAN, PyPI, and GitHub
Last checked20/09/2026
FeaturesIterative maximum diversity clustering to align batch-specific distributions, Extremely fast execution scaling linearly with millions of cells, Available in both R and Python (harmonypy) packages, Integrated natively into Seurat and Scanpy pipelines
Entry typeSoftware Library (R / Python)
Access modeOpen Source
AI roleIterative Dimensionality Alignment
Input dataNot recorded
Output dataNot recorded
Licence conditionsGPL-3.0
Commercial eligibilityPermissive open source release
Compute requirementsStandard CPU workstation
ValidationNot recorded
TypeSingle-cell batch integration algorithm
Intended useNot recorded
CompatibilityNot recorded
ManufacturerBroad Institute of MIT and Harvard
Biological applicationCross-tissue cell atlas integration, patient cohort harmonization, and multi-donor studies
Research workflowUncorrected PCA matrix -> Harmony batch alignment -> corrected embedding for clustering and UMAP
Evidence levelPeer-reviewed research (Nature Methods 2019) with thousands of citations
Integration evidencehttps://github.com/immunogenomics/harmony
Laboratory handoffProduces clean cell clusters for cell-type sorting and downstream validation