Clover-vis

Clover tool to mining differentially expressed genes (DEGs) in intaractive visualization tool. This tool helps to summarise gene feature of your intrust.

Installation

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

Run this app locally with:

python app.py

Open a browser at http://127.0.0.1:8050

Quick usase

Feature Data sources

• 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