https://github.com/greenelab/netscape
Exploring the network/pathway regularization landscape for gene expression data
https://github.com/greenelab/netscape
analysis gene-expression methodology networks pathways tool
Last synced: about 1 month ago
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Exploring the network/pathway regularization landscape for gene expression data
- Host: GitHub
- URL: https://github.com/greenelab/netscape
- Owner: greenelab
- License: bsd-3-clause
- Created: 2019-07-11T15:45:09.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2020-02-25T21:54:32.000Z (over 6 years ago)
- Last Synced: 2025-01-13T00:41:45.058Z (over 1 year ago)
- Topics: analysis, gene-expression, methodology, networks, pathways, tool
- Language: Jupyter Notebook
- Homepage:
- Size: 6.09 MB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# netscape
Exploring the **net**work/pathway regularization land**scape** 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](https://github.com/greenelab/BioBombe) for predicting gene
alteration status using TCGA gene expression data.
## Setup
We recommend using the conda environment specified in the `environment.yml` file to run these analyses. To build and activate this environment, run:
```shell
# conda version 4.5.0
conda env create --file environment.yml
conda activate netreg
```
To 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:
```R
library(devtools)
install_github('wgmao/PLIER')
```
You should then be able to run the `library(PLIER)` command
without errors.
## Running tests
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
```shell
pytest tests/
```
from the repo root.