Repositories list

• polygloty

  Public
  HTML

  •

  MIT License

  •0•2•0•1•Updated Jul 29, 2025Jul 29, 2025

• harpy

  Public
  Single-cell spatial proteomics analysis that makes you happy!

  machine-learningbioinformaticshpc+ 4spatialmicroscopyanalysis-frameworknapari-plugin

  Python

  •

  Other

  •7•34•14•2•Updated Jul 28, 2025Jul 28, 2025

• FlowSOM_Python

  Public
  The complete FlowSOM package known from R, now available in Python!

  machine-learningbioinformaticsclustering+ 1flowcytometry

  Python

  •

  GNU General Public License v3.0

  •5•22•2•1•Updated Jul 28, 2025Jul 28, 2025

• nichenetr

  Public
  NicheNet: predict active ligand-target links between interacting cells

  rna-seqgene-expressionnetwork-inference+ 7data-integrationsingle-cell-rna-seqsingle-cell-omicsintercellular-communicationligand-receptorligand-targetcell-cell-communication

  R

  •128•557•23•1•Updated Jul 23, 2025Jul 23, 2025

• iidx

  Public
  Interactive and interpretable differential expression modelling in cytometry

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 14, 2025Jul 14, 2025

• ViVAE

  Public
  Single-cell dimensionality reduction toolkit

  deep-learningdimensionality-reductionscrna-seq+ 4differential-geometrymdscytometrysingle-cell-analysis

  Jupyter Notebook

  •

  Apache License 2.0

  •1•7•0•0•Updated Jul 6, 2025Jul 6, 2025

• harpy_figures

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Jun 19, 2025Jun 19, 2025

• ViScore

  Public
  Single-cell dimensionality reduction evaluation and benchmarking toolkit

  benchmarkingdimensionality-reductionscrna-seq+ 2cytometrysingle-cell-analysis

  Python

  •

  Apache License 2.0

  •0•6•1•0•Updated May 31, 2025May 31, 2025

• napari-sparrow

  Public
  https://sparrow-pipeline.readthedocs.io/en/latest/

  Python

  •

  Other

  •0•29•13•1•Updated May 28, 2025May 28, 2025

• SingleBench

  Public
  Evaluation framework for exploratory modelling in cytometry

  R

  •

  MIT License

  •0•0•0•0•Updated May 16, 2025May 16, 2025

• PeacoQC

  Public
  Peak-based selection of high quality cytometry data

  R

  •9•17•3•0•Updated May 13, 2025May 13, 2025

• spotless-benchmark

  Public
  A repository for benchmarking spatial deconvolution and mapping tools

  R

  •

  MIT License

  •4•33•0•0•Updated May 13, 2025May 13, 2025

• ComputationalCytometry

  Public
  Workshop computational cytometry

  R

  •0•2•0•0•Updated Apr 15, 2025Apr 15, 2025

• nichenet_protocol

  Public
  HTML

  •

  MIT License

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

• CytoNorm

  Public
  R library to normalize cytometry data

  R

  •11•37•32•0•Updated Apr 1, 2025Apr 1, 2025

• FlowSOM

  Public
  Using self-organizing maps for visualization and interpretation of cytometry data

  R

  •8•29•5•0•Updated Mar 17, 2025Mar 17, 2025

• marble-sorter-ui

  Public
  Interface for the marble sorter

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• gradient-regularisation-interpretability

  Public
  Python

  •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• multinichenetr

  Public
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

  systems-biologyscrna-seqsingle-cell+ 9differential-expressionsingle-cell-rna-seqintercellular-communicationligand-receptorligand-targetcell-cell-interactioncell-cell-communication+ 2

  HTML

  •

  GNU General Public License v3.0

  •18•150•12•0•Updated Jan 14, 2025Jan 14, 2025

• hydra_hpc_example

  Public
  Hydra HPC example

  pythonhpcslurm+ 1hydra

  Python

  •0•5•0•0•Updated Dec 9, 2024Dec 9, 2024

• CytoBright

  Public
  Estimate Stain Index for single stained cytometry files.

  R

  •

  GNU General Public License v3.0

  •1•6•0•0•Updated Sep 27, 2024Sep 27, 2024

• nichenet_training

  Public
  R

  •1•1•0•0•Updated Sep 10, 2024Sep 10, 2024

• ExtractInfinicyt

  Public
  Script to extract fcs files and gating information from infinicyt .CYT files

  Java

  •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

• VIB_Hackathon_June_2024

  Public
  Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8T

  Jupyter Notebook

  •

  MIT License

  •4•2•2•0•Updated Jun 24, 2024Jun 24, 2024

• spatial_ccc_experiments

  Public
  Jupyter Notebook

  •

  MIT License

  •1•1•7•3•Updated Jun 13, 2024Jun 13, 2024

• synthspot

  Public
  synthspot: package to generate synthetic Visium-like spot data

  R

  •

  GNU General Public License v3.0

  •3•5•0•0•Updated May 16, 2024May 16, 2024

• cifconvert

  Public
  cifconvert is a package built on the python-bioformats package that saves images and masks from the proprietary Amnis CIF-file format to an HDF5 file.

  Python

  •

  GNU General Public License v3.0

  •1•1•0•3•Updated May 3, 2024May 3, 2024

• ViVAE_old

  Public
  Autoencoder-based models for dimension reduction of high-dimensional cytometry and single-cell RNA-seq data based on geometry and nearest-neighbour relations

  Python

  •

  Apache License 2.0

  •0•3•0•0•Updated Apr 26, 2024Apr 26, 2024

• GroupEnc

  Public
  Encoder with group loss for global structure preservation

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Dec 5, 2023Dec 5, 2023

• CytoNorm_note

  Public
  R code to demonstrate the functionalities of CytoNorm2.0

  R

  •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023