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    39 repositories

    • SpatialLeiden

      Public
      Implementation of multiplex Leiden for analysis of spatial omics data
      Python
      •
      GNU General Public License v3.0
      •0•17•3•0•Updated Feb 2, 2026Feb 2, 2026

    • computational-oncology-group

      Public
      HTML
      •1•1•0•0•Updated Jan 29, 2026Jan 29, 2026

    • ovrl.py

      Public
      A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.
      Python
      •
      Other
      •1•30•1•0•Updated Jan 27, 2026Jan 27, 2026

    • umi_alignment

      Public
      A snakemake pipeline for aligning UMI based WGS data and QC metrics associated with it
      Python
      •
      MIT License
      •0•1•10•1•Updated Jan 22, 2026Jan 22, 2026

    • multiSPAETI

      Public
      Implementation of MULTISPATI-PCA in Python
      Python
      •
      MIT License
      •1•4•0•0•Updated Jan 6, 2026Jan 6, 2026

    • sainsc

      Public
      Segmentation-free Analysis of In Situ Capture data
      Python
      •
      MIT License
      •0•13•0•1•Updated Jan 5, 2026Jan 5, 2026

    • EXLIQUID

      Public
      A code repository for the EXLIQUID data processing pipeline
      MIT License
      •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • ovrlpy-publication

      Public
      Code to reproduce ovrlpy paper
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Oct 14, 2025Oct 14, 2025

    • sonar

      Public
      Analytic and generative algorithm on co-occurrences in 2d maps
      MIT License
      •0•2•0•0•Updated Aug 31, 2025Aug 31, 2025

    • siNET_omics_analysis

      Public
      siNET_omics_analysis
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • panNEC_study2025

      Public
      Jupyter Notebook
      •1•0•0•0•Updated May 16, 2025May 16, 2025

    • sainsc-study

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Feb 18, 2025Feb 18, 2025

    • SpatialLeiden-Study

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Nov 25, 2024Nov 25, 2024

    • ssam

      Public archive
      Python
      •
      GNU Affero General Public License v3.0
      •11•27•5•0•Updated Oct 12, 2024Oct 12, 2024

    • ssam-lite

      Public
      HTML
      •
      MIT License
      •1•2•13•0•Updated Apr 12, 2023Apr 12, 2023

    • planktonpy

      Public
      Analysis platform for spatial point processes in python
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Dec 9, 2022Dec 9, 2022

    • preeclamspsia_Nonn_etal

      Public
      A repository for code used to analyse data and create figures presented in Nonn et al., 2022 describing the single cell spatio-temporal landscape of placenta ti…
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 6, 2022Dec 6, 2022

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.8k•0•0•0•Updated Jul 27, 2022Jul 27, 2022

    • ssam_example

      Public
      SSAM examples
      Jupyter Notebook
      •2•2•6•0•Updated Jan 8, 2022Jan 8, 2022

    • hmap

      Public
      Python package for hierarchical clustering and plotting of heatmaps
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 15, 2021Dec 15, 2021

    • ssam-lite-server

      Public
      JavaScript
      •
      MIT License
      •1•0•1•0•Updated Oct 4, 2021Oct 4, 2021

    • TumourMix

      Public
      A tumour heterogenity analyser using the concepts of Baysien Gaussian Mixture Model
      0•0•1•0•Updated Aug 10, 2021Aug 10, 2021

    • gelviz

      Public
      A python package for plotting genomic elements in a genome browser style
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 1, 2021Mar 1, 2021

    • geanno

      Public
      Python package for the annotation of genomic elements.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 19, 2021Feb 19, 2021

    • pygorich

      Public
      A python package for Gene Set Enrichment Analyses
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 16, 2021Feb 16, 2021

    • pCyto

      Public
      Python package for plotting ideograms
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 15, 2021Feb 15, 2021

    • CRC_scRNAseq

      Public
      Code for analysing single-cell data from colorectal cancer organoids
      Jupyter Notebook
      •4•3•0•0•Updated Feb 10, 2021Feb 10, 2021

    • htslib-js

      Public
      CMake
      •
      GNU Lesser General Public License v3.0
      •1•10•1•0•Updated Jun 14, 2020Jun 14, 2020

    • PDAC_scRNAseq

      Public
      Code for analysing single-cell sequencing data from PDAC organoids
      1•0•0•0•Updated Apr 27, 2020Apr 27, 2020

    • diSPIM_screen

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Mar 25, 2020Mar 25, 2020