DILiS-lab's repositories
pyproteonet
Python package for imputation, peptide-to-protein aggregation as well as in silico data creation of proteomics data with a specific focus on the development and evaluation of imputation methods in proteomics. Also provides proteomics specific imputation methods based on graph neural networks.
GNN_imputer
Graph Neural Network Driven Imputation of Missing Abundances in Mass Spectrometry-Based Proteomics
opt-synthdata-4tl
This is the code repository for the paper "Optimizing ODE-derived Synthetic Data for Transfer Learning in Dynamical Biological Systems".
pepermint
Graph Neural Network for Peptide Abundance Imputation in MS Proteomics Data
pmotif_analytics
Collection of tools to run analyses based on the pmotif_lib py-package
pmotif_lib
Perform motif detection, either with traditional frequency, or with positional metrics for each graphlet occurrence.
SimbaML
SimbaML is an all-in-one framework for integrating prior knowledge of ODE models into the ML process by synthetic data augmentation. It allows for the convenient generation of realistic synthetic data by sparsifying and adding noise. Furthermore, our framework provides customizable pipelines for various ML experiments, such as transfer learning.