Exploring the network/pathway regularization landscape for gene expression data
Overall goal of this project: evaluate network regularized methods for a variety of practical problems using a variety of biological networks.
At present, this repo contains an adaptation of the pipeline used in BioBombe for predicting gene alteration status using TCGA gene expression data.
We recommend using the conda environment specified in the environment.yml file to run these analyses. To build and activate this environment, run:
# conda version 4.5.0
conda env create --file environment.yml
conda activate netregTo run PLIER, you'll have to install it from GitHub using the
devtools library. Run the following from an R interactive shell/
REPL inside the netreg Conda environment:
library(devtools)
install_github('wgmao/PLIER')
You should then be able to run the library(PLIER) command
without errors.
Running the tests requires the pytest module (included in the specified
Conda environment). Once this module is installed, you can run the tests
by executing the command
pytest tests/from the repo root.