Clover

0. ChangeLog

Please see ChangeLog.md

1. Overview

Clover is a tool for prioritising rare genes in a differentially expressed gene (DEG) list.

2. Installation

2.1. Requirements

• Python 3.8 or higher Other requirements are listed in requirements.txt.

To run Clover, clone this repository and move to the repository in your terminal / Command Prompt.

git clone https://github.com/G708/Clover.git
cd Clover

The project relies on several Python packages. You can install these dependencies like this:

pip install -r requirements.txt

Download the data with:

python src/data_prep.py

3. Quick usage

This tool can use as command line tool and interactive dashboard application.

3.1 Command line tool

To run Clover as command line tool, run this command:

python src/Clover.py -i test_imput_DEG.csv --id_type hgnc_symbol -o test_output

Output

The output files are as below:

Clover
└──test_output
  ├──  rank_result.csv
  └── wordcloud
    ├── FDR.png
    ├── Glint.png
    ├── Dowsing.png
    ├── Treasure_Hunt.png
    └── Ropeway.png

3.1.1 Essential options

To run command line tool, you need to specify input file with -i option. This input file should be a csv file with FDR columns. For full options, please refer to function page.

-i, --input

Input expression matrix file with FDR columns. Default delimiter of the file is , , but user can specify by the additional option --sep.

--id_type

gene name / ID type in input file to convert ID and merge the columns. Choose from {hgnc_symbol, ensembl_gene_id, entrezgene_id}. Default is hgnc_symbol.

3.2. Interactive Dash tool

For interactive dashboard application, we implemented clover using Dash.

Please check the https://github.com/G708/clover-dash repository for more details.

4. Feature Data sources

Download the data with:

python src/data_prep.py

Data sources information

• RNA-seq data from Genotype-Tissue Expression GTEx project v8 (THE GTEX CONSORTIUM, 2020) data in Human protein Atlas (https://www.proteinatlas.org/download/rna_tissue_gtex.tsv.zip).
• Publication data for each gene is publicly available at https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz.
• Score of DE prior is downloaded from

  Crow,M. et al. (2019) Predictability of human differential gene expression. Proceedings of the National Academy of Sciences, 116, 6491–6500. https://doi.org/10.1073/pnas.1802973116

5. Citation

Oba GM, Nakato R. Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach. Genes Cells. 2024 Apr 11. doi: 10.1111/gtc.13119. Epub ahead of print. PMID: 38602264.

6. License

This project is licensed under the terms of the MIT license.