kchen-lab / lad

Visualization and analysis of single-cell RNA-seq data by alternative clustering

System requirements

• Software dependencies:
  • Windows/Linux/Mac OS (tested on Windows 10)
  • R (>=4.0.0; tested on 4.3.1)
  • Seurat (>=5.0.0; tested on 5.0.0)

Installation

• R can be downloaded here: https://www.r-project.org/. We recommend R studio for easier data exploration: https://www.rstudio.com/categories/rstudio-ide/. (~5 minutes)
• Seurat can be installed here (~5 minutes)
• LAD does not require installation. It can be run directly by loading it with source("R/lad_seurat.R") and run with RunALT (see examples for details).

Examples

Dataset	Item	File
	Implementation of BCD for Seurat	bcd_seurat.R
	BCD and Euclidean	simulation.Rmd/nb.html
Simulation	Seurat integration	simulation_seurat_integration.Rmd/nb.html
	Harmony	simulation_harmony_integration.Rmd/nb.html
	BCD and Euclidean	gse118614_10x_all.Rmd/nb.html
Retina	Seurat integration	gse118614_10x_all_seurat_integration.Rmd/nb.html
	Harmony	gse118614_10x_all_harmony_integration.Rmd/nb.html
	BCD and Euclidean	gse145926.Rmd/nb.html
Covid-19	Seurat integration	gse145926-seurat-integration.Rmd/nb.html
	Harmony	gse145926-harmony.Rmd/nb.html
	BCD and Euclidean	lung.Rmd/nb.html
Lung	Seurat integration	lung_seurat_integration.Rmd/nb.html
	Harmony	lung_harmony_integration.Rmd/nb.html

Data

Processed data for the Lung example can be found here.