# MM-PD1

**Repository Path**: plainTHS/mm-pd1

## Basic Information

- **Project Name**: MM-PD1
- **Description**: R and Python scripts used to replicate results of manuscript. 
- **Primary Language**: R
- **License**: CC-BY-4.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-11-06
- **Last Updated**: 2024-11-17

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# MM-PD1

### Description
R and Python scripts used to replicate results of manuscript. 

### Script list
* R scripts
> * Figures.R: Steps of generate Figures.
> * FUN.R: functions used to produce results.

* Python Scripts
> * MoleculerDocking.py: Molecular docking script.

### File list
*  1. Differential expression genes list
> * GSE91061_diffRes.rda
> * PRJEB23709_diffRes.rda

* 2. Alternative combinations of gene-panel
> * alterCombine4.rda, combination of four genes
> * alterCombine3.rda, combination of three genes

* 3. data *gExprSurv.rda* provides a data.frame including Survival info of 98 patients and 75 commone genes expresison data in dataset of __[GSE91061](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE91061)__. *All_SurvDat.rda* provides a data.frame of Survival info and final genes for datasets of GSE91061, GSE78220,  PRJEB23709, and Braun_2020. *datExpr0.rda* is a matrix data of top 10000 differential expression genes.

* 4. data *PredDat2014RES_GSE91061.rda* provides a list of drug sensitivity analyzed results.

* 5. Files in directory __CTDdb__: _Target chemicals interactive with genes APP, ARHGAP42, GSTA4 and UCHL1. Data queried on Aug 2024._

### Acknowledgments
* [ggpubr](https://github.com/kassambara/ggpubr)
* [clusterProfiler](https://github.com/GuangchuangYu/clusterProfiler)
* [pROC](https://github.com/xrobin/pROC)
* [survival](https://github.com/therneau/survival)
* [smina](https://github.com/quantori/scip-smina)