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    132 repositories

    • nf-modules

      Public
      Python
      •
      MIT License
      •0•1•0•2•Updated Mar 17, 2026Mar 17, 2026

    • schard

      Public
      reticulate-free single cell format conversion
      R
      •
      GNU General Public License v3.0
      •15•209•0•0•Updated Mar 16, 2026Mar 16, 2026

    • dockage

      Public
      Cellgeni Docker files
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Mar 16, 2026Mar 16, 2026

    • py8rds

      Public
      R Data Deserialization in python
      Jupyter Notebook
      •
      MIT License
      •0•7•0•0•Updated Mar 16, 2026Mar 16, 2026

    • Image-ST

      Public
      A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
      Python
      •
      MIT License
      •3•3•0•0•Updated Mar 12, 2026Mar 12, 2026

    • fetch-series

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 12, 2026Mar 12, 2026

    • nf-atac

      Public
      Pipeline to process sc-ATAC data with pyCistopic
      pythonbioinformaticspipeline
      pythonbioinformaticspipelinenextflowatac-seqsingle-cellsingle-cell-atac-seqsingle-cell-multiomicsmultiome
      Python
      •
      MIT License
      •0•3•0•0•Updated Mar 12, 2026Mar 12, 2026

    • webatlas-pipeline

      Public
      A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
      Python
      •
      MIT License
      •11•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • farmer

      Public
      Slack bot that tells you the status of your LSF jobs 🧑‍🌾
      Python
      •
      GNU Affero General Public License v3.0
      •0•3•2•0•Updated Mar 2, 2026Mar 2, 2026

    • nf-demultiplex

      Public
      Our Souporcell repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Feb 27, 2026Feb 27, 2026

    • nf-scVI-metrics

      Public
      Grid search to optimise hyperparameters for scVI
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 25, 2026Feb 25, 2026

    • reprocess_public_10x

      Public
      Scripts to help get fastqs
      Shell
      •
      GNU General Public License v3.0
      •3•19•4•0•Updated Feb 24, 2026Feb 24, 2026

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•11•1•1•Updated Feb 21, 2026Feb 21, 2026

    • sceasy

      Public
      A package to help convert different single-cell data formats to each other
      R
      •
      GNU General Public License v3.0
      •68•460•44•5•Updated Feb 20, 2026Feb 20, 2026

    • STARsolo

      Public
      wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
      Shell
      •
      GNU General Public License v3.0
      •9•80•3•0•Updated Feb 18, 2026Feb 18, 2026

    • AKOYA_analysis

      Public
      set of codes for analysis of sptaial proteomics datasets
      Jupyter Notebook
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • ovary

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • spatialproteomics

      Public
      Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly multiplexed immunohistoch…
      Python
      •
      MIT License
      •8•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • nf-scsajr

      Public
      single cell alternative splicing
      R
      •0•2•0•0•Updated Feb 11, 2026Feb 11, 2026

    • nf-irods-to-fastq

      Public
      Get CRAMs from iRODS and convert them to FASTQ
      Nextflow
      •
      MIT License
      •2•2•1•0•Updated Feb 10, 2026Feb 10, 2026

    • xenium_velocyto

      Public
      An attempt to use nuclear/cytoplasmic transcripts from Xenium as unspliced/spliced for velocyto
      Jupyter Notebook
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • nf-cellbender

      Public
      Nextflow implementation of Cellbender
      R
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • OMERO_tools

      Public
      Python
      •0•1•0•0•Updated Feb 3, 2026Feb 3, 2026

    • nf-larry

      Public
      Python
      •0•2•0•0•Updated Feb 2, 2026Feb 2, 2026

    • h5ad-cli

      Public
      A CLI for operations with AnnData objects in .h5ad and .zarr files
      h5zarranndata
      h5zarranndatah5ad
      Python
      •
      MIT License
      •0•6•2•0•Updated Jan 27, 2026Jan 27, 2026

    • docs

      Public
      CellGen IT documentation
      docswikireadthedocs
      docswikireadthedocssanger
      MIT License
      •4•1•0•0•Updated Jan 23, 2026Jan 23, 2026

    • ondemand

      Public
      Supercomputing. Seamlessly. Open, Interactive HPC Via the Web
      JavaScript
      •
      MIT License
      •173•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • xenium_vistools

      Public
      visualisation codes for Xenium experiments
      Jupyter Notebook
      •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

    • segger_dev

      Public
      a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segme…
      HTML
      •
      MIT License
      •13•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • reprocess_irods_upload

      Public
      A repo with collection of scripts and notebooks which where used to validate and upload datasets to IRODS
      Jupyter Notebook
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025