Clover

0. ChangeLog

Please see ChangeLog.md

1. Overview

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

2. Installation

2.1. Requirements

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

To run this app locally, clone this repository and open this app folder in your terminal/Command Prompt.

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

The project relies on several Python packages including Dash, Dash Bootstrap Components, Plotly, and Pandas. You can install these dependencies like this:

pip install -r requirements.txt

Download the data with:

python src/data_prep.py

3. Quick usase

This tool can use as command line tool and web application.

3.1 Command line tool

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

python clover.py -i imput_DEG_list.csv --id_type hgnc_symbol

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 this 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 repository name repository for more details.

4. Feature Data sources

Download the data with:

python src/data_prep.py

• 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

• Human cell line essentiality data is downloaded from OGEE (https://v3.ogee.info/#/home)

  S. Gurumayum *, P. Jiang *, X. Hao, T.L Campos, N.D. Young, P.K. Korhonen, R.B. Gasser, P. Bork, X.M. Zhao, L.J. He, Chen, W.-H. (2020). "OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Research, gkaa884, doi: 10.1093/nar/gkaa884

5. Reference

• Preprint

6. License

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