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    78 repositories

    • nichenetpy

      Public
      rna-seqgene-expressionnetwork-inference
      rna-seqgene-expressionnetwork-inferencedata-integrationsingle-cell-rna-seqsingle-cell-omicsintercellular-communicationligand-receptorligand-targetcell-cell-communication
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•22•6•1•Updated Oct 23, 2026Oct 23, 2026

    • harpy

      Public
      Single-cell spatial omics analysis that makes you happy!
      machine-learningbioinformaticshpc
      machine-learningbioinformaticshpcspatialmicroscopyanalysis-frameworkspatialdataspatial-omics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•78•35•2•Updated Oct 23, 2026Oct 23, 2026

    • FlowSOM_Python

      Public
      The complete FlowSOM package known from R, now available in Python!
      machine-learningbioinformaticsclustering
      machine-learningbioinformaticsclusteringflowcytometry
      Python
      •
      GNU General Public License v3.0
      •7•35•3•5•Updated Oct 19, 2026Oct 19, 2026

    • pddshap

      Public
      Python
      •1•1•0•0•Updated Oct 16, 2026Oct 16, 2026

    • ExtractInfinicyt

      Public
      Script to extract fcs files and gating information from infinicyt .CYT files
      Java
      •1•2•0•0•Updated Oct 5, 2026Oct 5, 2026

    • FlowSOM

      Public
      Using self-organizing maps for visualization and interpretation of cytometry data
      R
      •9•37•6•0•Updated Sep 30, 2026Sep 30, 2026

    • nichenetr

      Public
      NicheNet: predict active ligand-target links between interacting cells
      rna-seqgene-expressionnetwork-inference
      rna-seqgene-expressionnetwork-inferencedata-integrationsingle-cell-rna-seqsingle-cell-omicsintercellular-communicationligand-receptorligand-targetcell-cell-communication
      R
      •134•681•26•0•Updated Sep 25, 2026Sep 25, 2026

    • napari-sparrow

      Public
      https://sparrow-pipeline.readthedocs.io/en/latest/
      Python
      •
      Other
      •0•34•13•1•Updated Sep 23, 2026Sep 23, 2026

    • iidx

      Public
      Interactive and interpretable differential expression modelling in cytometry
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 15, 2026Sep 15, 2026

    • ViScore

      Public
      Single-cell dimensionality reduction evaluation and benchmarking toolkit
      benchmarkingdimensionality-reductionscrna-seq
      benchmarkingdimensionality-reductionscrna-seqcytometrysingle-cell-analysis
      Python
      •
      Apache License 2.0
      •1•12•1•0•Updated Sep 4, 2026Sep 4, 2026

    • ViVAE

      Public
      Single-cell dimensionality reduction toolkit
      deep-learningdimensionality-reductionscrna-seq
      deep-learningdimensionality-reductionscrna-seqdifferential-geometrymdscytometrysingle-cell-analysis
      Jupyter Notebook
      •
      Apache License 2.0
      •2•11•0•0•Updated Sep 4, 2026Sep 4, 2026

    • ecosystem-packages

      Public
      Registry for scverse ecosystem packages
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •97•0•0•0•Updated Sep 2, 2026Sep 2, 2026

    • CytoBright

      Public
      Estimate Stain Index for single stained cytometry files.
      R
      •
      GNU General Public License v3.0
      •1•7•0•1•Updated Aug 20, 2026Aug 20, 2026

    • sparrow-notebooks

      Public
      Repo to store the large tutorial notebooks of the SPArrOW package
      0•0•2•0•Updated Aug 19, 2026Aug 19, 2026

    • CytoNorm

      Public
      R library to normalize cytometry data
      R
      •12•41•33•0•Updated Jul 7, 2026Jul 7, 2026

    • MedialAxisMapping

      Public
      Global alignment of CLEM images based on blood vessel patterns
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 28, 2026May 28, 2026

    • BonteEtAl_AML_Dx_EuroFlow

      Public
      Code for the paper Bonte S et al. Old data, new tricks: Comprehensive computational analysis of 10 years of multi-center EuroFlow acute myeloid leukemia diagnos…
      R
      •0•0•0•0•Updated Apr 29, 2026Apr 29, 2026

    • OrgaCCC

      Public
      Python
      •1•0•0•0•Updated Apr 28, 2026Apr 28, 2026

    • GCNLA

      Public
      Python
      •1•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • DSFCM_meeting2026

      Public
      Scripts that were used to analyze the shared dataset during the “One Dataset, Many Perspectives: Flow Cytometry Analysis Workflows” DSFCM meeting
      0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • nichenet_protocol

      Public
      HTML
      •
      MIT License
      •1•5•1•0•Updated Apr 15, 2026Apr 15, 2026

    • marble-sorter-ui

      Public
      Interface for the marble sorter
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • PeacoQC

      Public
      Peak-based selection of high quality cytometry data
      R
      •12•23•3•0•Updated Feb 23, 2026Feb 23, 2026

    • harpy_figures

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Feb 11, 2026Feb 11, 2026

    • adversarial-mri

      Public
      Triggering hallucinations in model-based MRI reconstruction via adversarial perturbations
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • ComputationalCytometry

      Public
      Workshop computational cytometry
      R
      •2•3•0•0•Updated Jan 19, 2026Jan 19, 2026

    • PIDgeon

      Public
      PIDgeon: pipeline for processing cytometry data after PID screening with generation of patient reports
      Jupyter Notebook
      •0•3•0•0•Updated Jan 8, 2026Jan 8, 2026

    • TENET

      Public
      Python
      •1•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • CeSpGRN

      Public
      CeSpGRN: Inferring cell specific GRN using single-cell gene expression data
      Python
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Oct 21, 2025Oct 21, 2025

    • FAIR2025_Tutorial_TRACE

      Public
      Data exploration and visualisation of cytometry data with TRACE
      Python
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
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