Motivation | Prerequisites | Cell line data | Initialize a Harmony object | L_2 scaling to induce cosine distance | Initial clustering | Evaluating initial cluster diversity | Maximum-diversity soft-clustering | Diverse cluster assignment | Cluster centroid estimation | Correction | Mixture of Experts model | Estimate MoE model parameters | Cell specific corrections | Multiple iterations of Harmony | Session info

Introduction | Installation | Integrating cell line datasets from 10X | Next Steps | Interfacing to software packages | Detailed breakdown of the Harmony algorithm | Session Info

Introduction | Generating the dataset | Create SeuratObject | (Optional) Download original data | Running Harmony | Calculate PCA cell embeddings | Perform an integrated analysis using harmony | Using harmony embeddings for dimensionality reduction in Seurat | Perform clustering using the harmonized vectors of cells | TSNE dimensionality reduction | UMAP