https://github.com/bhklab/statinemt
Project to regenerate the pharmacogenomics analysis in this paper: "Statin-induced cancer cell death can be mechanistically uncoupled from prenylation of RAS family proteins"
https://github.com/bhklab/statinemt
analysis
Last synced: 4 months ago
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Project to regenerate the pharmacogenomics analysis in this paper: "Statin-induced cancer cell death can be mechanistically uncoupled from prenylation of RAS family proteins"
- Host: GitHub
- URL: https://github.com/bhklab/statinemt
- Owner: bhklab
- Created: 2017-02-20T16:14:59.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2017-10-30T18:47:41.000Z (over 7 years ago)
- Last Synced: 2024-12-30T03:21:50.301Z (6 months ago)
- Topics: analysis
- Language: R
- Homepage: https://www.ncbi.nlm.nih.gov/pubmed/22413970
- Size: 346 KB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# StatinEMT
## Introduction
This is a project to regenerate the pharmacogenomics analysis in this paper:
"Statin-induced cancer cell death can be mechanistically uncoupled from prenylation of RAS family proteins"
citation's info to be added
The script for the analysis is written in R.
----
## Dependencies:
These R packages need to be installed in order to run the analysis script:
- Biobase
- PharmacoGx
- mixtools
- mclust
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## Reproducibility of the Analysis:
- Once the project is downloaded to the user computer, the user needs to navigate to the main directory of the project "StatinEMT-master".
- Inside the main directory, there is an R script file named "Script_EMT_Figures_Informatics.R". Running this script will regenerate the full pharmacogenomics analysis of the paper.
**Important Note:** the user needs to set the working directory inside the script file before running it, i.e. change the following code inside the script:
`StatinEMT_Directory <- NULL`
to
`StatinEMT_Directory <- "./pathToStatinEMT-master_Directory"`
- Running the script will produce all the figures related to the pharmacogenomics analysis
- Included in the project are the bimodality scores for all genes across CCLE cell lines that have RNA-seq data. This can be found in "./data/BimodalScores_All_Genes.RData"