- 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)
- 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 withRunALT(see examples for details).
| 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 |
Processed data for the Lung example can be found here.