Repositories list

• RNA-KG

  Public
  Collection of tutorials to build RNA-KG v2.0 from scratch and for reproducing experiments such as "context-aware" KG pruning, clustering, and link prediction.

  bioinformaticsdatabaserna+ 1

  bioinformaticsdatabasernakg

  Jupyter Notebook

  •

  Apache License 2.0

  •2•29•1•0•Updated Mar 16, 2026Mar 16, 2026

• schemalink-docs

  Public
  Source code for the documentation website of the Schemalink project

  docsschemalink

  docsschemalink

  Ruby

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•1•Updated Jan 26, 2026Jan 26, 2026

• tide-var

  Public
  Ensemble of deep neural networks for the prediction of pathogenic variants in Mendelian diseases

  Python

  •1•0•0•0•Updated Jan 21, 2026Jan 21, 2026

• ncRNA-CUPID

  Public
  ncRNA-CUPID, Computational Understanding of Pairwise Interactions in ncRNA Data (matchmaking for ncRNAs)

  Jupyter Notebook

  •

  Apache License 2.0

  •0•3•0•0•Updated Jan 7, 2026Jan 7, 2026

• Bioinformatics_practice

  Public
  Project assignment for the Bioinformatics Master Course

  Jupyter Notebook

  •0•1•0•0•Updated Nov 13, 2025Nov 13, 2025

• miRInter-Trans

  Public
  A transformer-based model to predict micro RNA interactions

  Jupyter Notebook

  •

  Apache License 2.0

  •0•1•0•0•Updated Nov 4, 2025Nov 4, 2025

• ensmallen

  Public
  🍇 Ensmallen is the Rust/Python high-performance graph processing submodule of the GRAPE library.

  pythonprocessingrust+ 1

  pythonprocessingrustgraph

  Python

  •

  MIT License

  •14•40•10•1•Updated Sep 29, 2025Sep 29, 2025

• RNA_m5C_predict

  Public
  Deep‑learning inference for cytosine 5‑methylation in Human RNA sequences

  Python

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• full_transformer_rna_rna

  Public
  standard seq2seq transformer model with encoder, decoder, and cross-attention, for RNA-RNA interaction modelling

  Python

  •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

• grape_helper_lib

  Public
  Collection of function to improve GRAPE functionality

  Python

  •0•0•0•0•Updated May 28, 2025May 28, 2025

• mosclust

  Public
  Stability based methods for model order selection in clustering problems.

  R

  •0•0•0•0•Updated May 23, 2025May 23, 2025

• clusterv

  Public
  The clusterv R package implements a set of functions to assess the reliability of clusters discovered by clustering algorithms.

  R

  •0•0•0•0•Updated May 12, 2025May 12, 2025

• Finenzyme

  Public
  Language modeling for enzyme sequences

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 28, 2025Apr 28, 2025

• RNA-KG_homogeneous_emb_analysis

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Apr 14, 2025Apr 14, 2025

• missSNF

  Public
  R implementation of the miss-SNF algorithm.

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• hetnode2vec_ensmallen

  Public
  This repository provides an implementation to add Het-node2vec as a library to Grape.

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• DR_omics_integration

  Public
  code and material to run all the experiments for dimensionality reduction guided by block analysis, data integration, OS prediction

  R

  •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• grape

  Public
  🍇 GRAPE is a Rust/Python Graph Representation Learning library for Predictions and Evaluations

  machine-learninggraphhigh-performance+ 1

  machine-learninggraphhigh-performanceknowledge-graph

  Jupyter Notebook

  •

  MIT License

  •39•622•37•0•Updated Feb 24, 2024Feb 24, 2024

• sHAM

  Public
  Compact representations of convolutional neural networks via weight pruning and quantization

  compressiondeep-learningneural-network+ 1

  compressiondeep-learningneural-networkneural-network-compression

  Python

  •

  Apache License 2.0

  •3•10•0•0•Updated Jul 18, 2023Jul 18, 2023

• obogaf-parser

  Public
  a perl5 module to handle obo and gaf file

  Perl

  •

  Other

  •1•0•0•0•Updated Oct 14, 2022Oct 14, 2022

• godata-pipe

  Public
  a pipeline to build datasets for GO terms prediction

  Perl

  •

  Other

  •1•0•0•0•Updated Oct 14, 2022Oct 14, 2022

• hemdag

  Public
  an R package implementing several Hierarchical Ensemble Methods for graphs

  R

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Oct 14, 2022Oct 14, 2022

• grape.github.io

  Public
  Repository for the GraPE project website.

  Python

  •1•1•1•0•Updated Jul 8, 2022Jul 8, 2022

• epigenomic_dataset

  Public
  Python package wrapping ENCODE epigenomic data for a number of reference cell lines.

  Jupyter Notebook

  •1•6•0•0•Updated Apr 21, 2022Apr 21, 2022

• parSMURF-NG

  Public
  C++

  •

  Other

  •1•0•0•0•Updated Feb 24, 2022Feb 24, 2022

• meta_models

  Public
  Python package with common meta-models building blocks.

  HTML

  •

  MIT License

  •0•1•0•0•Updated Apr 27, 2021Apr 27, 2021

• crr_prediction

  Public
  Prediction of activation of cis-regulatory regions.

  Jupyter Notebook

  •0•0•0•0•Updated Apr 27, 2021Apr 27, 2021

• DataAnalysisR

  Public
  A tool for statistical analysis, imputation via missForest, identification of most important variables

  R

  •

  MIT License

  •0•3•0•0•Updated Mar 17, 2021Mar 17, 2021

• parSMURF

  Public
  High Performance Computing imbalance-aware machine learning tool for the genome-wide detection of pathogenic variants

  Python

  •

  GNU General Public License v3.0

  •2•7•3•0•Updated Dec 8, 2020Dec 8, 2020

• MicroscopyImageAnalysis

  Public
  Published code for immunohistochemical image segmentation and co-occurrence analysis

  MATLAB

  •0•0•0•0•Updated Dec 5, 2020Dec 5, 2020