Awesome Cancer recurrence prediction of Multiple Myeloma DREAM challenge v2 created by jkobject.
This pipeline shows various simple ML models used to predict patient with Multiple Myeloma at high risk of relapse from transcriptomics profiles. From a comprehensive litterature review I came up with a set of genes, genesets and clinical information to use as predictors.
3 Models are shown together with some metrics and used to define strengths and weaknesses of each.
The default model selected for prediction is a logistic regression with elasticnet penalty, an l1_ratio of 1.0 and a constraint term of 0.2.
Information about the literature review, my work schedule and process during this 10h mini-project are available in NOTEBOOK.md
git clone https://github.com/jkobject/MM_DREAM.git
cd MM_DREAM
pip install -e .A dockerized version is also available
docker pull jkobject/mm_dream#look at example.py !
from mm_dream import main
clf = main(syn_login, syn_password)or
python -m mm_dream $syn_login $syn_password
#or
docker run -it jkobject/mm_dream $syn_login $syn_password#look at example.py for more info!
from mm_dream import main
clf = main(syn_login, syn_password)
res = clf.predict(X, Y)or
python mm_dream $syn_login $syn_password $rna_path $clinical_path
#or
docker run -it jkobject/mm_dream $syn_login $syn_password $rna_path $clinical_path
#extract the file out with cp
docker cp <containerId>:/app/mm_dream /host/path/targetthe results will be in new_predictions.csv
Read the CONTRIBUTING.md file.
Lets take a look at the structure of this template:
├── Containerfile # The file to build a container using buildah or docker
├── CONTRIBUTING.md # Onboarding instructions for new contributors
├── docs # Documentation site (add more .md files here)
│ └── index.md # The index page for the docs site
├── .github # Github metadata for repository
│ ├── release_message.sh # A script to generate a release message
│ └── workflows # The CI pipeline for Github Actions
├── .gitignore # A list of files to ignore when pushing to Github
├── LICENSE # The license for the project
├── Makefile # A collection of utilities to manage the project
├── MANIFEST.in # A list of files to include in a package
├── mkdocs.yml # Configuration for documentation site
├── mm_dream # The main python package for the project
│ ├── base.py # The base module for the project
│ ├── __init__.py # This tells Python that this is a package
│ ├── __main__.py # The entry point for the project
│ └── VERSION # The version for the project is kept in a static file
├── README.md # The main readme for the project
├── setup.py # The setup.py file for installing and packaging the project
├── requirements.txt # An empty file to hold the requirements for the project
├── requirements-test.txt # List of requirements for testing and devlopment
├── setup.py # The setup.py file for installing and packaging the project
└── tests # Unit tests for the project (add mote tests files here)
├── conftest.py # Configuration, hooks and fixtures for pytest
├── __init__.py # This tells Python that this is a test package
└── test_base.py # The base test case for the project
All the utilities for the template and project are on the Makefile
❯ make
Usage: make <target>
Targets:
help: ## Show the help.
install: ## Install the project in dev mode.
fmt: ## Format code using black & isort.
lint: ## Run pep8, black, mypy linters.
test: lint ## Run tests and generate coverage report.
watch: ## Run tests on every change.
clean: ## Clean unused files.
virtualenv: ## Create a virtual environment.
release: ## Create a new tag for release.
docs: ## Build the documentation.
switch-to-poetry: ## Switch to poetry package manager.
init: ## Initialize the project based on an application template.