# Fast, Sensitive, and Accurate Integration of Single Cell Data

## Documentation for package ‘harmony’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cell_lines | List of metadata table and scaled PCs matrix
cell_lines_small | Same as cell_lines but smaller (300 cells).
harmony | Harmony: fast, accurate, and robust single cell integration.
HarmonyMatrix | A proxy call to 'RunHarmony()'. Deprecated.
harmony_options | Set advanced options for RunHarmony
moe_ridge_get_betas | Get beta Utility
pbmc.ctrl | Gene expression data of control PBMC from Kang et al. 2017. This contains a sample of 1000 cells from that condition and is used for the Seurat Vignette.
pbmc.stim | Gene expression data of stimulated PBMC from Kang et al. 2017. This contains a sample of 1000 cells from that condition and is used for the Seurat Vignette.
RunHarmony | Generic function that runs the harmony algorithm on single-cell genomics cell embeddings.
RunHarmony.default | This is the primary harmony interface.
RunHarmony.Seurat | Applies harmony on a Seurat object cell embedding.
RunHarmony.SingleCellExperiment | Applies harmony on PCA cell embeddings of a SingleCellExperiment.