Software

Omics data

• 

  08OCT 2026

  Omics data

  scXMatch

  Python package for quantification of global distributions shifts in multivariate data.Python package for quantification of global distributions shifts in multivariate data.

  Read more about scXMatch
• 

  11SEP 2026

  Omics data

  SignifiKANTE

  Python package for fast P-value computation for GRNs inferred from transcriptomics data.Python package for fast P-value computation for GRNs inferred from transcriptomics data.

  Read more about SignifiKANTE
• 

  08DEC 2025

  Omics data

  SwitchTFI

  Python package to infer GRNs and key transcription factors involved in cell state transitions from scRNA-seq data.Python package to infer GRNs and key transcription factors involved in cell state transitions from scRNA-seq data.

  Read more about SwitchTFI
• 

  16JUL 2025

  Omics data

  KINference

  R tool to infer differential kinase-substrate links from phosphoproteomics data.R tool to infer differential kinase-substrate links from phosphoproteomics data.

  Read more about KINference
• 

  05DEC 2024

  Omics data

  DysRegNet

  Python tool to infer single-sample gene dysregulation events from gene expression data.Python tool to infer single-sample gene dysregulation events from gene expression data.

  Read more about DysRegNet
• 

  05DEC 2024

  Omics data

  SHouT

  Python tool to quantify tissue heterogeneity based on spatial omics data.Python tool to quantify tissue heterogeneity based on spatial omics data.

  Read more about SHouT
• 

  03MAY 2023

  Omics data

  TF-Prioritizer

  Pipeline to prioritize condition-specific transcription factors from multimodal omics data.Pipeline to prioritize condition-specific transcription factors from multimodal omics data.

  Read more about TF-Prioritizer
• 

  12DEC 2020

  Omics data

  BiCoN

  Python package for network-constrained biclustering of gene expression data.Python package for network-constrained biclustering of gene expression data.

  Read more about BiCoN

Interaction data and gene signatures

• 

  05JUN 2024

  Interaction data and gene signatures

  Drugst.One

  Plugin to turn genes lists into drug repurposing web tools with interactive network visualization.Plugin to turn genes lists into drug repurposing web tools with interactive network visualization.

  Read more about Drugst.One
• 

  27JUN 2022

  Interaction data and gene signatures

  DIGEST

  Web tool and Python package to quantify functional coherence of gene sets and networks.Web tool and Python package to quantify functional coherence of gene sets and networks.

  Read more about DIGEST
• 

  04JAN 2022

  Interaction data and gene signatures

  ROBUST

  Web service and Python tool for computing disease modules that are robust to random and study bias.Web service and Python tool for computing disease modules that are robust to random and study bias.

  Read more about ROBUST
• 

  04NOV 2021

  Interaction data and gene signatures

  NeDRex

  Interactive network medicine platform for disease module identification and drug repurposing.Interactive network medicine platform for disease module identification and drug repurposing.

  Read more about NeDRex
• 

  12JUN 2020

  Interaction data and gene signatures

  CoVex

  Online network medicine platform to explore virus-host-drug interactions for SARS-CoV-2 and SARS-CoV-1.Online network medicine platform to explore virus-host-drug interactions for SARS-CoV-2 and SARS-CoV-1.

  Read more about CoVex

Benchmarking and bias mitigation

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  08APR 2025

  Benchmarking and bias mitigation

  DataSAIL

  Python package for leakage-reduced data splitting to enable realistic ML model evaluation.Python package for leakage-reduced data splitting to enable realistic ML model evaluation.

  Read more about DataSAIL
• 

  06MAR 2024

  Benchmarking and bias mitigation

  confinspect

  Python test suite to assess the effect of demographic confounders on GRN inference.Python test suite to assess the effect of demographic confounders on GRN inference.

  Read more about confinspect
• 

  25AUG 2021

  Benchmarking and bias mitigation

  AIMe

  Web registry for reporting biomedical AI systems.Web registry for reporting biomedical AI systems.

  Read more about AIMe
• 

  29MAR 2021

  Benchmarking and bias mitigation

  Test suite for active module identification methods

  Python test suite for benchmarking active module identification methods.Python test suite for benchmarking active module identification methods.

  Read more about Test suite for active module identification methods

Genetic variants

• 

  11SEP 2026

  Genetic variants

  GNExT

  Framework for web-based exploration of GWAS summary statistics.Framework for web-based exploration of GWAS summary statistics.

  Read more about GNExT
• 

  16JUL 2024

  Genetic variants

  Epistasis Disease Atlas

  Web tool for interactive exploration of putative epistatic interactions in eight complex diseases.Web tool for interactive exploration of putative epistatic interactions in eight complex diseases.

  Read more about Epistasis Disease Atlas
• 

  16JUL 2024

  Genetic variants

  NeEDL

  Command line tool for network-based epistasis detection in complex diseases.Command line tool for network-based epistasis detection in complex diseases.

  Read more about NeEDL
• 

  14APR 2020

  Genetic variants

  EpiGEN

  Python pipeline for simulation of genetic epistasis.Python pipeline for simulation of genetic epistasis.

  Read more about EpiGEN

Federated learning

• 

  07DEC 2021

  Federated learning

  Federated SVD

  Tool for federated and privacy-preserving singular value decomposition.Tool for federated and privacy-preserving singular value decomposition.

  Read more about Federated SVD
• 

  22NOV 2021

  Federated learning

  Flimma

  Tool for federated privacy-preserving differential gene expression analysis.Tool for federated privacy-preserving differential gene expression analysis.

  Read more about Flimma

Miscellaneous

• 

  25NOV 2025

  Miscellaneous

  NApy

  Python package for fast and memory-efficient statistical testing in the presence of missing data.Python package for fast and memory-efficient statistical testing in the presence of missing data.

  Read more about NApy
• 

  28JUN 2023

  Miscellaneous

  GraphSimViz

  Web service for quantification of biases in disease association data.Web service for quantification of biases in disease association data.

  Read more about GraphSimViz
• 

  18MAY 2023

  Miscellaneous

  CorrNet

  Python package for the analysis of historical correspondence networks.Python package for the analysis of historical correspondence networks.

  Read more about CorrNet
• 

  16MAY 2019

  Miscellaneous

  GEDLIB

  C++ library for exact and approximate graph edit distance computation.C++ library for exact and approximate graph edit distance computation.

  Read more about GEDLIB