Changelog

All notable changes to this project will be documented in this file.The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

March 2024

Hyperparameter tuning
Changed default latent distribution from "normal" to logit normal ("ln")

January 2024

sccoral in sc-verse cookiecutter template
Added sccoral.data for project-specific data
Added callbacks for pretraining procecure

Tests

Added tests for model setup
Added tests based on implemented tests for callbacks
Added tests for misc. model features

Model

Added custom TrainingPlan with pre-training procedure for covariates

Documentation

Add readthedocs website

December 2023

Model/Module/nn - Covariate informed VAE with linear decoder, model based on LSCVI
Added l1-regularization term to linear decoder

[TODO]

Project data

Implement data projection

Jupyter Notebooks

Jupyter Notebook - Demonstration on simulated data
Jupyter Notebook - Demonstration on IFN stimulation - Kang et al, 2018 data

tl

Find markers

Plotting (.pl)

Implement plotting module

Refactoring