SCMMIB pipeline for 65 benchmark methods

Introduction

This SCMMIB_pipeline folder is a sub-project of SCMMIB project. The main project github folder is at https://github.com/bm2-lab/SCMMI_Benchmark.

SCMMIB_pipeline contains:

1. preprocessing_scripts: including scripts to generate the gene activity matrix and downsample and scalability simulation datasets from all benchmark datasets, and a introduction to these scripts.

2. envs: including conda environment yaml files for 40 benchmark algorithms, and an example to use the env files.

3. wdl_workflow: including the wdl worklfow file and input json file for all benchmark method, and an example for input json configuration.

4. benchmark_methods: including task specific module scripts for 6 single-cell multimodal integration types. These scripts can be executed with uniform pipeline of wdl_workflow and algorithm specific envs.

The output of all benchmark methods can be evaluated with scmmib python package in our project folder https://github.com/bm2-lab/SCMMI_Benchmark.

Data availablity

The pre-processed project data (h5ad, rds and rSeurat format) is available at figshare folder (https://figshare.com/articles/dataset/SCMMIB_Register_Report_Stage_2_processed_datasets/27161451/2). Simluation datasets in SCMMIB study can be generated from R scripts in the data_simulation folder.

Tutorials

1. Tutorial for reproducing all methods and all tasks in SCMMIB project tutorial 1.

2. Tutorial for applying scmmib pipeline to new integration methods tutorial 2.

3. Tutorial for applying scmmib pipeline to new benchmark datasets tutorial 3.

Citation

Stage 1 manuscript

Fu, Shaliu; Wang, Shuguang; Si, Duanmiao; Li, Gaoyang; Gao, Yawei; Liu, Qi (2024). Benchmarking single-cell multi-modal data integrations. figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.26789572.v1

Datasets

SCMMIB project processed datasets. figshare. Dataset. https://doi.org/10.6084/m9.figshare.27161451.v2