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"
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Keywords
Repository
Project to regenerate the pharmacogenomics analysis in this paper: "Statin-induced cancer cell death can be mechanistically uncoupled from prenylation of RAS family proteins"
Basic Info
- Host: GitHub
- Owner: bhklab
- Language: R
- Default Branch: master
- Homepage: https://www.ncbi.nlm.nih.gov/pubmed/22413970
- Size: 346 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
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
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 "ScriptEMTFigures_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/BimodalScoresAllGenes.RData"
Owner
- Name: BHKLAB
- Login: bhklab
- Kind: organization
- Location: Toronto, Ontario, Canada
- Website: http://www.pmgenomics.ca/bhklab/
- Repositories: 168
- Profile: https://github.com/bhklab
The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre
GitHub Events
Total
Last Year
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| ba3lwi | b****i@g****m | 9 |
| Wail Ba alawi | w****l@o****a | 7 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0