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    33 repositories

    • 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•0•Updated Apr 14, 2026Apr 14, 2026

    • schemalink-api

      Public
      Source code for the API of the Schemalink project
      apischemalink
      apischemalink
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Mar 24, 2026Mar 24, 2026

    • 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
      bioinformaticsdatabasernakg
      Jupyter Notebook
      •
      Apache License 2.0
      •2•29•1•0•Updated Mar 16, 2026Mar 16, 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

    • schemalink-webapp

      Public
      Source code for the webapp of the Schemalink project
      webappschemalink
      webappschemalink
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•1•15•0•Updated Oct 22, 2025Oct 22, 2025

    • ensmallen

      Public
      🍇 Ensmallen is the Rust/Python high-performance graph processing submodule of the GRAPE library.
      pythonprocessingrust
      pythonprocessingrustgraph
      Python
      •
      MIT License
      •14•40•11•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
      machine-learninggraphhigh-performanceknowledge-graph
      Jupyter Notebook
      •
      MIT License
      •39•626•37•0•Updated Feb 24, 2024Feb 24, 2024

    • sHAM

      Public
      Compact representations of convolutional neural networks via weight pruning and quantization
      compressiondeep-learningneural-network
      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
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