This page displays information for the following method:

Name:

Harmony

Description:

PCA and clustering-based correction

GitHub:

immunogenomics/harmony

DOI:

10.1038/s41592-019-0619-0

Labels required?:

No

1 Overall

1.1 Plot

1.2 Table

2 Individual metrics

2.1 Overall

2.2 Batch correction

Batch correction

PCR batch

Batch ASW

Graph iLISI

Graph connectivity

kBET

2.3 Bio conservation

Bio conservation

NMI cluster/label

ARI cluster/label

Label ASW

Isolated label F1

Isolated label silhouette

Graph cLISI

HVG conservation

Cell cycle conservation

Trajectory conservation

3 Embeddings

Dataset (Output)

simulations_1_1 (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

immune_cell_hum (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

simulations_2 (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

pancreas (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

mouse_brain (Embedding)

Input features (Scaling)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

lung_atlas (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

immune_cell_hum_mou (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

4 Scalability

4.1 Time

4.2 Memory