https://github.com/bhklab/cfi402257
Delay of mitotic progression caused by impairment of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer
https://github.com/bhklab/cfi402257
analysis
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Delay of mitotic progression caused by impairment of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer
- Host: GitHub
- URL: https://github.com/bhklab/cfi402257
- Owner: bhklab
- Created: 2017-11-07T11:46:52.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-12-29T18:07:21.000Z (over 7 years ago)
- Last Synced: 2024-12-30T03:20:58.890Z (5 months ago)
- Topics: analysis
- Language: R
- Size: 6.55 MB
- Stars: 0
- Watchers: 6
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# CFI402257
Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer
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Abstract
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Citation
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To cite this work in publication, use
Reproducibility of the Analysis Results
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1. Set up the software environment
2. Download pSets
3. Run the R scripts
Set up the software environment
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Analysis of this paper has been done in the following session environment. So to reproduce all the paper results the same session should be prepared by installing all the mentioned packages.
#sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] fgsea_1.4.0 Rcpp_0.12.14 piano_1.18.0 gridExtra_2.3 gplots_3.0.1 ggplot2_2.2.1 PharmacoGx_1.8.2
[8] Biobase_2.38.0 BiocGenerics_0.24.0
Download pSets
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These pSets are required to be accessible for the scripts in a directory named data/PSets:
UHNBreast_PSet
CCLE_Pset
Run the R scripts
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#pipeline_to_associate_drugResponse_with_geneList.R:
Script aims to find associations between a given drug and geneList of interest.
*This script takes some time to be completed as it finds univariate associations between all genes and the drug response. Then, it will measure the enrichemnt of geneList in the list of all genes ranked by their univariate associations. More details of the method are provided in the paper mentioned above.
User needs to modify the script and set the working directory to "./CFI402257-master/"
The script is already set with a general example of using the UHNBreast_PSet to find associations between Paclitaxel and anaphase-promoting complex gene set.