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@cellgeni

Cellular Genomics Informatics

Wellcome Sanger Institute

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  1. STARsolo STARsolo Public

    wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq

    Shell 75 8

  2. reprocess_public_10x reprocess_public_10x Public

    Scripts to help get fastqs

    Shell 15 3

  3. c2l c2l Public

    Set of scripts to run cell2location on farm

    Jupyter Notebook 2

  4. nf-cellbender nf-cellbender Public

    Nextflow implementation of Cellbender

    R

  5. sceasy sceasy Public

    A package to help convert different single-cell data formats to each other

    R 452 67

  6. schard schard Public

    reticulate-free single cell format conversion

    R 201 13

Repositories

Showing 10 of 127 repositories
  • h5ad-cli Public
    cellgeni/h5ad-cli’s past year of commit activity
    Python 0 0 0 0 Updated Jan 14, 2026
  • farmer Public

    Slack bot that tells you the status of your LSF jobs 🧑‍🌾

    cellgeni/farmer’s past year of commit activity
    Python 3 AGPL-3.0 0 2 0 Updated Jan 13, 2026
  • Image-ST Public

    A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode

    cellgeni/Image-ST’s past year of commit activity
    Python 3 MIT 2 0 0 Updated Jan 9, 2026
  • nf-modules Public
    cellgeni/nf-modules’s past year of commit activity
    Python 1 MIT 0 0 3 Updated Jan 8, 2026
  • dockage Public

    Cellgeni Docker files

    cellgeni/dockage’s past year of commit activity
    Dockerfile 3 AGPL-3.0 0 0 0 Updated Jan 8, 2026
  • schard Public

    reticulate-free single cell format conversion

    cellgeni/schard’s past year of commit activity
    R 201 GPL-3.0 13 1 0 Updated Jan 7, 2026
  • docs Public

    CellGen IT documentation

    cellgeni/docs’s past year of commit activity
    1 MIT 4 0 0 Updated Jan 5, 2026
  • segger_dev Public Forked from EliHei2/segger_dev

    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).

    cellgeni/segger_dev’s past year of commit activity
    HTML 0 MIT 12 0 0 Updated Dec 16, 2025
  • nf-scautoqc Public

    Nextflow implementation of scAutoQC pipeline

    cellgeni/nf-scautoqc’s past year of commit activity
    Python 10 GPL-3.0 0 1 1 Updated Dec 5, 2025
  • reprocess_irods_upload Public

    A repo with collection of scripts and notebooks which where used to validate and upload datasets to IRODS

    cellgeni/reprocess_irods_upload’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 1, 2025
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