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PerturBase

Description

We present PerturBase, the most comprehensive database designed for the analysis and visualization of single-cell perturbation datasets (http://www.perturbase.cn/). PerturBase collects 122 datasets from 46 publicly research studies, covering 115 single-modal and 7 multi-modal datasets that include 24,254 genetic and 230 chemical perturbations from about approximately 5 million cells.

To demonstrate the readability, reusability, and reproducibility of our single-cell perturbation data preprocess and analysis workflow, we provided a demo case.

Requirements

R_env.yaml, Python_env.yaml are the R_env and Python_env packages used in the pipeline_bash_files. Please first install them in your environment.

Demo Data

Due to the size exceeding GitHub's limitations, demo data is hosted at Figshare. To run through our standard preprocess workflow, please execute the following commands with the demo data.

Specifically, for RNA-seq and ATAC-seq, please organize the files as follows,

Demo_data
├── RNA
│   ├── raw.h5ad
│   
│   
├── ATAC
    ├── fragment.tsv.gz
    ├── fragment.tsv.gz.tbi
    ├── cbc_perturbation_dict.tsv

pipeline_bash_files

Here is where we store the code for processing workflows of different types of raw data. You can use this code to replicate our results. Especially for our demo data:

For ATAC-seq fragment data set,

bash ATAC_fragment_all.sh /path_to_your_file/Demo_data/ATAC Hs

For RNA-seq data set,

bash RNA_all.sh  /path_to_your_file/Demo_data/RNA  Hs

Before executing the script, please replace Python_env, R_env, Script_base_path, msigdb_Signature_path, etc., with the paths on your local machine.

scripts

Scripts that is invoked by the main program, i.e, pipeline_bash_files.

MsigDB_signature

Molecular signatures used in PerturBase

Reproducibility

This manuscript reproduce_the_result_of_mixscape.py is the code for reproducing the extended Data of Fig.9a of Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens. We use the manuscript evaluate_the_impact_of_hvg.py to evaluate the impact of the selection of hvg in data preprocessing on the perturbation-specific differentially expressed genes.

Bug Report

Any question is welcome in the issue.

Citation

Zhiting Wei, Duanmiao Si, Qi Liu et al. PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization, 2024.

Contacts

[email protected] [email protected] [email protected]