Software

Network inference

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  08DEC 2025

  Network Inference

  SwitchTFI

  Python package to infer transition gene regulatory networks and key transcription factors involved in cell state transitions from scRNA-seq data.Python package to infer transition gene regulatory networks and key transcription factors involved in cell state transitions from scRNA-seq data.

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  16JUL 2025

  Network Inference

  KINference

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

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  05DEC 2024

  Network Inference

  DysRegNet

  Python tool to infer gene dysregulation events for individual samples in comparison to a control condition from gene expression data.Python tool to infer gene dysregulation events for individual samples in comparison to a control condition from gene expression data.

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  06MAR 2024

  Network Inference

  BoostDiff

  BoostDiff is a Python tool to infer differential gene regulatory networks from gene expression data.BoostDiff is a Python tool to infer differential gene regulatory networks from gene expression data.

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  03MAY 2023

  Network Inference

  TF-Prioritizer

  TF-Prioritizer is an automated pipeline that prioritizes condition-specific transcription factors from multimodal data and generates an interactive web report.  It accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activityTF-Prioritizer is an automated pipeline that prioritizes condition-specific transcription factors from multimodal data and generates an interactive web report.  It accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activity

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Network exploration and disease module mining

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  05JUN 2024

  Network Exploration and Disease Module Mining

  Drugst.One

  Plugin to turn your tool that outputs a list of genes or proteins into a feature rich, drug repurposing web tool with interactive network visualization.Plugin to turn your tool that outputs a list of genes or proteins into a feature rich, drug repurposing web tool with interactive network visualization.

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  04JAN 2022

  Network Exploration and Disease Module Mining

  ROBUST

  ROBUST is a Python tool which uses enumeration of diverse prize-collecting Steiner trees to compute disease modules that are robust to random bias.ROBUST is a Python tool which uses enumeration of diverse prize-collecting Steiner trees to compute disease modules that are robust to random bias.

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  04NOV 2021

  Network Exploration and Disease Module Mining

  NeDRex

  NeDRex (network-based drug repurposing and exploration) is an interactive network medicine platform for disease module identification and drug repurposing.NeDRex (network-based drug repurposing and exploration) is an interactive network medicine platform for disease module identification and drug repurposing.

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  12DEC 2020

  Network Exploration and Disease Module Mining

  BiCoN

  BiCoN allows to stratify patients while elucidating disease mechanisms. BiCoN is a network-constrained biclustering approach, which restricts biclusters to functionally related genes connected in molecular networks and maximizes the expression difference between two groups of patients.BiCoN allows to stratify patients while elucidating disease mechanisms. BiCoN is a network-constrained biclustering approach, which restricts biclusters to functionally related genes connected in molecular networks and maximizes the expression difference between two groups of patients.

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  12JUN 2020

  Network Exploration and Disease Module Mining

  CoVex

  CoVex is a unique online network and systems medicine platform for data analysis that integrates virus-human interactions for SARS-CoV-2 and SARS-CoV-1. It implements different network-based approaches for the identification of new drug targets and new repurposable drugs.CoVex is a unique online network and systems medicine platform for data analysis that integrates virus-human interactions for SARS-CoV-2 and SARS-CoV-1. It implements different network-based approaches for the identification of new drug targets and new repurposable drugs.

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Benchmarking and bias mitigation

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  08APR 2025

  Benchmarking and Bias Mitigation

  DataSAIL

  Python package that facilitates leakage-reduced data splitting to enable realistic evaluation of ML models that are intended to be used in out-of-distribution scenarios.Python package that facilitates leakage-reduced data splitting to enable realistic evaluation of ML models that are intended to be used in out-of-distribution scenarios.

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  06MAR 2024

  Benchmarking and Bias Mitigation

  confinspect

  Our Python test suite confinspect allows to assess the effect of demographic confounders such as sex and age on methods for inferring gene regulatory and gene co-expression networks.Our Python test suite confinspect allows to assess the effect of demographic confounders such as sex and age on methods for inferring gene regulatory and gene co-expression networks.

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  27JUN 2022

  Benchmarking and Bias Mitigation

  DIGEST

  DIGEST is a systems medicine tool for the in silico validation of gene and disease sets, clusterings, and subnetworks w.r.t. genetic and functional coherence. It is available as a web service, as a Python package, and via a REST API.DIGEST is a systems medicine tool for the in silico validation of gene and disease sets, clusterings, and subnetworks w.r.t. genetic and functional coherence. It is available as a web service, as a Python package, and via a REST API.

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  25AUG 2021

  Benchmarking and Bias Mitigation

  AIMe

  The AIMe registry for artificial intelligence in biomedical research is a community-driven platform for reporting biomedical AI systems. It allows authors of new biomedical AIs to report their models in an explicit and transparent fashion and thereby fosters comparability and reproducibility.The AIMe registry for artificial intelligence in biomedical research is a community-driven platform for reporting biomedical AI systems. It allows authors of new biomedical AIs to report their models in an explicit and transparent fashion and thereby fosters comparability and reproducibility.

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  29MAR 2021

  Benchmarking and Bias Mitigation

  Test Suite for Active Module Identification Methods

  A Python suite for testing the functional relevance of the results produced by active module identification methods, as well as their robustness to random pertubations of the employed protein-protein interaction networks.A Python suite for testing the functional relevance of the results produced by active module identification methods, as well as their robustness to random pertubations of the employed protein-protein interaction networks.

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Epistasis

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  16JUL 2024

  Epistasis

  Epistasis Disease Atlas

  Web tool for interactive exploration of putative epistatic interactions in eight complex diseases (late-onset Alzheimer’s disease, bipolar disorder, coronary artery disease, hypertension, type-1 diabetes, type-2 diabetes, rheumatoid arthritis, inflammatory bowel disease).Web tool for interactive exploration of putative epistatic interactions in eight complex diseases (late-onset Alzheimer’s disease, bipolar disorder, coronary artery disease, hypertension, type-1 diabetes, type-2 diabetes, rheumatoid arthritis, inflammatory bowel disease).

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  16JUL 2024

  Epistasis

  NeEDL

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

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  14APR 2020

  Epistasis

  EpiGEN

  EpiGEN is an easy-to-use epistasis simulation pipeline written in Python. It supports epistasis models of arbitrary size, the specification of the minor allele frequencies for both noise and disease SNPs, and  the simulation of observation bias.EpiGEN is an easy-to-use epistasis simulation pipeline written in Python. It supports epistasis models of arbitrary size, the specification of the minor allele frequencies for both noise and disease SNPs, and  the simulation of observation bias.

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Federated learning

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  07DEC 2021

  Federated Learning

  Fever-PCA

  Fever-PCA (federated principal component analysis for vertically partitioned data) is a federated, privacy-preserving tool for principal component analysis, including patient stratification and dimensionality reduction.Fever-PCA (federated principal component analysis for vertically partitioned data) is a federated, privacy-preserving tool for principal component analysis, including patient stratification and dimensionality reduction.

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  22NOV 2021

  Federated Learning

  Flimma

  Flimma is a privacy-preserving hybrid federated tool for differential gene expression analysis. Flimma by design preserves the privacy of the local data, since the expression profiles never leave the local execution sites and shared meta-parameters are protected via secure multi-party computation.Flimma is a privacy-preserving hybrid federated tool for differential gene expression analysis. Flimma by design preserves the privacy of the local data, since the expression profiles never leave the local execution sites and shared meta-parameters are protected via secure multi-party computation.

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Miscellaneous

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  25NOV 2025

  Miscellaneous

  NApy

  Python package with Numba and OpenMP-powered C++ backends for fast and memory-efficient statistical testing in the presence of missing data.Python package with Numba and OpenMP-powered C++ backends for fast and memory-efficient statistical testing in the presence of missing data.

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  05DEC 2024

  Miscellaneous

  SHouT

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

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  28JUN 2023

  Miscellaneous

  GraphSimViz

  GraphSimViz is a web service for quantification of biases phenotype-based disease definitions introduce in disease association data.GraphSimViz is a web service for quantification of biases phenotype-based disease definitions introduce in disease association data.

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  18MAY 2023

  Miscellaneous

  CorrNet

  CorrNet is a Python package for the analysis of historical correspondence networks.CorrNet is a Python package for the analysis of historical correspondence networks.

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  16MAY 2019

  Miscellaneous

  GEDLIB

  GEDLIB is an easily extensible C++ library for (suboptimally) computing the graph edit distance (GED) between two labeled graphs. GEDLIB implements more than thirty state-of-the-art methods for computing GED and comes with predefined edit costs for some benchmark datasets.GEDLIB is an easily extensible C++ library for (suboptimally) computing the graph edit distance (GED) between two labeled graphs. GEDLIB implements more than thirty state-of-the-art methods for computing GED and comes with predefined edit costs for some benchmark datasets.

  Read more about GEDLIB