https://github.com/jamesyang007/ghostbasil
GhostKnockoff + BASIL
https://github.com/jamesyang007/ghostbasil
Last synced: 3 months ago
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GhostKnockoff + BASIL
- Host: GitHub
- URL: https://github.com/jamesyang007/ghostbasil
- Owner: JamesYang007
- Created: 2022-05-02T22:34:51.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2023-05-28T19:35:20.000Z (over 2 years ago)
- Last Synced: 2025-05-12T19:22:30.239Z (5 months ago)
- Language: C++
- Size: 3.56 MB
- Stars: 2
- Watchers: 3
- Forks: 3
- Open Issues: 6
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Metadata Files:
- Readme: README.md
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README
# GhostBASIL
This is a repository for experimental code using GhostKnockoff and BASIL framework
for fast and efficient LASSO fitting on high-dimensional data.
Specifically, this library is created with the intention of applying it on GWAS summary statistics.
## Dependencies
- [Bazel](https://docs.bazel.build/versions/main/install.html)
## Developer Installation
Run the following command to generate machine-specific `.bazelrc`:
```
./generate_bazelrc
```
Then, install the developement dependencies:
```
mamba update -y conda
mamba env create
conda activate ghostbasil
```
Our tools require `omp` to be installed on the system.
On Mac, it must be installed with Homebrew as our build system assumes:
```
brew install libomp
```
See the following for installations of each of the sub-packages:
- [R README](R/README.md)
- [C++ README](ghostbasil/README.md)
## References
- [Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies](https://www.biorxiv.org/content/10.1101/2021.12.06.471440v1)
- [A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009141)