Skip to content

@cellgeni Cellular Genomics Informatics

Change the repository type filter

All

    Repositories list

    127 repositories

    • schard

      Public
      reticulate-free single cell format conversion
      R
      •
      GNU General Public License v3.0
      •13•201•1•0•Updated Jan 7, 2026Jan 7, 2026

    • dockage

      Public
      Cellgeni Docker files
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Jan 6, 2026Jan 6, 2026

    • docs

      Public
      CellGen IT documentation
      docswikireadthedocssanger
      MIT License
      •4•1•0•0•Updated Jan 5, 2026Jan 5, 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 segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).
      HTML
      •
      MIT License
      •12•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • h5ad-cli

      Public
      Python
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • nf-modules

      Public
      Python
      •
      MIT License
      •0•1•0•3•Updated Dec 9, 2025Dec 9, 2025

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•10•1•1•Updated Dec 5, 2025Dec 5, 2025

    • Image-ST

      Public
      A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
      Python
      •
      MIT License
      •2•3•0•0•Updated Dec 4, 2025Dec 4, 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

    • tic-4101

      Public
      Python
      •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

    • hackathon

      Public
      Python
      •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

    • nf-irods-to-fastq

      Public
      Get CRAMs from iRODS and convert them to FASTQ
      Nextflow
      •
      MIT License
      •2•2•1•0•Updated Nov 27, 2025Nov 27, 2025

    • nf-upload2irods

      Public
      Pipeline for uploading files to iRODS system
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • notebooks

      Public
      Cellular Genetics Informatics Notebooks
      notebooks
      HTML
      •
      GNU General Public License v3.0
      •14•24•2•0•Updated Nov 7, 2025Nov 7, 2025

    • xenium_velocyto

      Public
      An attempt to use nuclear/cytoplasmic transcripts from Xenium as unspliced/spliced for velocyto
      Jupyter Notebook
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • bulk_rnaseq

      Public
      Wrapper scripts for convenient processing of bulk RNA-seq experiments
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Oct 22, 2025Oct 22, 2025

    • nf-cellbender

      Public
      Nextflow implementation of Cellbender
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • nf-metacells

      Public
      Python
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • nf-processed2irods

      Public
      Pipeline to move processed datasets to irods
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • nf-atac

      Public
      Pipeline to process sc-ATAC data with pyCistopic
      pythonbioinformaticspipelinenextflowatac-seqsingle-cellsingle-cell-atac-seqsingle-cell-multiomicsmultiome
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 14, 2025Oct 14, 2025

    • reprocess_public_10x

      Public
      Scripts to help get fastqs
      Shell
      •
      GNU General Public License v3.0
      •3•15•3•0•Updated Oct 7, 2025Oct 7, 2025

    • ticket-3970

      Public
      Scripts for integration of Xenium datasets
      Jupyter Notebook
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • nf-reprocessing-public-10x

      Public
      Nextflow pipeline of Alex's reprocessing scripts
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 24, 2025Sep 24, 2025

    • cells2visium

      Public
      segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells
      Python
      •
      MIT License
      •2•2•0•0•Updated Sep 24, 2025Sep 24, 2025

    • Spatial_Hackathon_2025

      Public
      Genome Campus Spatial Hackathon
      Python
      •1•0•0•2•Updated Sep 24, 2025Sep 24, 2025

    • nf-larry

      Public
      Python
      •0•2•0•0•Updated Sep 15, 2025Sep 15, 2025

    • scsajr

      Public
      R package for nf-scsajr
      HTML
      •
      Other
      •0•2•0•0•Updated Sep 9, 2025Sep 9, 2025

    • spatialxe

      Public
      Nextflow
      •
      MIT License
      •9•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • watergate

      Public
      Wiretaps for things
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 4, 2025Sep 4, 2025

    • nf-c2l

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 27, 2025Aug 27, 2025