clover-dash

0. ChangeLog

Please see ChangeLog.md

1. Overview

Clover is tool for prioritising rare genes in a differentially expressed gene (DEG) list. We used this tool to rank DEGs from bulk RNA-seq analysis, but any gene list with an FDR value (statistically significant value of differentially expressed) is applicable.

2. Installation

Everything is contained in a docker image. To install docker, please see here.

docker pull g7o8/clover-dash

3. Usage

To run the docker image, please use the following command:

docker run --rm -p 8050:8050 clover-dash

Then, open your browser and go to http://localhost:8050/. After that, follow the instruction to run Clover.

4. Input

The input file is eather CSV or TSV file with the gene name (HGNC Symbol) or id (Entrez Gene ID, Ensembl Gene ID) and FDR columns. The header is required.

5. Function

In the clover-dash dashboard, you can do the following:

5.1 Home page

• Run Clover with your input file and calculate the Glint, Dowsing, Treasure Hunt, and Ropeway for each gene.
• Download the result as a csv file.
• Generate WordClouds for each ranking.

5.2 Data Sources page

• Interact with the Clover database. i.e.) Exproler interested gene in DE prior, Gini index, and number of publications distribution plots.

5. Output

The output file is a csv file with the gene name (HGNC Symbol), gene id (Entrez Gene ID, Ensembl Gene ID), FDR, Glint, Dowsing, Treasure Hunt, and Ropeway columns. Also able to download plots using plotly function.

6. Citation

If you use Clover or clover-dash, please cite the following:

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.