https://github.com/GenoML/genoml

Core pipeline of GenoML
https://github.com/GenoML/genoml

Last synced: 3 months ago
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Core pipeline of GenoML

• Host: GitHub
• URL: https://github.com/GenoML/genoml
• Owner: GenoML
• License: apache-2.0
• Created: 2019-02-27T00:03:41.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2020-08-03T13:49:33.000Z (almost 4 years ago)
• Last Synced: 2024-01-17T20:47:26.505Z (5 months ago)
• Language: R
• Homepage: https://genoml.com
• Size: 25.6 MB
• Stars: 14
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome_automl_libraries - GenoML - an Automated Machine Learning (AutoML) for Genomics (Genomics)

README

        
# GenoML-core

GenoML is an Automated Machine Learning (AutoML) for Genomic. This is the core package of GenoML. 

this repo is under development, please report any issues (bug, performance, documentation) on the [GenoML issues page](https://github.com/GenoML/genoml/issues). 

Here are some quick "get started" exmaples, please checkout the additional options and details in the [Usage][] and [CLI][].

In general, use linux or mac with python > 3.5 for best results.

## Install 

Run:

~~~~

pip install genoml

~~~~

## Train the ML model 

You can use the IPDGC (International Parkinson's Disease Genomics Consortium) test data. This data is a simulation of the genetic and clinical data used for Parkinson's diagnosis in previous publications. You can find it at [IPDGC example data][].

Download and unzip data:

~~~

wget https://github.com/ipdgc/GenoML-Brief-Intro/raw/master/exampleData.zip

unzip exampleData.zip 

~~~

To train, run:

~~~~

genoml-train --geno-prefix=./exampleData/training --pheno-file=./exampleData/training.pheno --model-dir=./exampleModel

~~~~

Final tuned model and performance metrics are stored in the ```--model-dir``` directory. 

## Using the trained ML model for inference

~~~~

genoml-inference --model-dir=./exampleModel --valid-dir=./exampleData --valid-geno-prefix=./exampleData/validation --valid-pheno-file=./exampleData/validation.pheno

~~~~

Valdiation results and model performance metrics are stored in the ```--valid-dir``` directory. 

> For debugging purposes, include the ```-v``` or ```-vvv``` flags at the end of a command.

[usage]: https://genoml.github.io/docs/usage

[CLI]: https://genoml.github.io/docs/cli

[IPDGC example data]: https://github.com/ipdgc/GenoML-Brief-Intro/raw/master/exampleData.zip

     

## Report issues 

Please report any issue or suggestions on the [GenoML issues page](https://github.com/GenoML/genoml/issues).