Comprehensive benchmark of dimension reduction methods for single-cell data analysis
August 18, 2023 ยท View on GitHub
Software requirements
- Nextflow
- Docker or Singularity
The list of benchmarking datasets
- scATAC-seq: https://1drv.ms/x/s!AuDfAP0z9Zsma9Hsr9Ggoz3MtFU?e=0RKKLU
- scRNA-seq:
- scHi-C:
How to prepare new benchmark datasets
Benchmark data is stored in anndata format. The anndata object should contain:
adata.X: cell by feature count matrix. For scATAC-seq, the format of feature names should be:chr:start-end.adata.obs["cell_annotation"]: cluster/cell-type annotation of each barcode.data.obs['batch']: batch annotation of each barcode (optional).
How to run benchmark
The pipeline uses docker or singularity containers to run the benchmark. Therefore, you need to install either docker or singularity on your machine. The pipeline needs to download large data files, so make sure you have enough disk space (>20G) and a fast internet connection.
Use ./bench.sh -profile singularity or ./bench.sh -profile docker to run benchmarks.
The benchmark results will be stored in ./results folder.
See nextflow.config for additional configuration options.