This page displays information for the following dataset:

Name:

 simulations_2

Description:

 Simulation with nested batch effects

Type:

 Simulated RNA

Cells:

 19318

Batches:

 16

Labels:

 4

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

Method (Output)

Harmony (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

scGen* (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

scANVI* (Embedding)

Input features (Scaling)

Full (Unscaled)

HVG (Unscaled)

FastMNN (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

Seurat v3 CCA (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

trVAE (Embedding)

Input features (Scaling)

Full (Unscaled)

HVG (Unscaled)

FastMNN (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

MNN (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

BBKNN (Graph)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

Scanorama (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

LIGER (Embedding)

Input features (Scaling)

Full (Unscaled)

HVG (Unscaled)

Scanorama (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

ComBat (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

scVI (Embedding)

Input features (Scaling)

Full (Unscaled)

HVG (Unscaled)

Conos (Graph)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

DESC (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

SAUCIE (Features)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

SAUCIE (Embedding)

Input features (Scaling)

Full (Scaled)

Full (Unscaled)

HVG (Scaled)

HVG (Unscaled)

Unintegrated (Features)

Input features (Scaling)

Full (Unscaled)

4 Scalability

4.1 Time

4.2 Memory