Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq.
See how to use Harmony with your data and integrate it into your analysis pipeline.
Find out more about the internal data structures and algorithm details in this tutorial.
Visualize how Harmony aligns single-cell RNA-seq datasets from three different donors.
The easiest way to get Harmony is to install it from Github:
Harmony has been tested on R versions >= 3.4 on Linux, macOS, and Windows.
HarmonyMatrix() function on your PCs from principal component analysis:
library(harmony) harmonized_pcs <- HarmonyMatrix( data_mat = pcs, # Matrix with coordinates for each cell (row) along many PCs (columns) meta_data = meta_data, # Dataframe with information for each cell (row) vars_use = "dataset", # Column in meta_data that defines dataset for each cell do_pca = FALSE # Since we are providing PCs, do not run PCA )
If you use Harmony for published work, please cite our manuscript:
Fast, sensitive, and accurate integration of single cell data with Harmony
Ilya Korsunsky, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri
bioRxiv 2019. doi.org/10.1101/461954
We will share the code needed to reproduce results from the manuscript at https://github.com/immunogenomics/harmony2019.