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@cellgeni

Cellular Genetics 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 50 6

  2. reprocess_public_10x reprocess_public_10x Public

    Scripts to help get fastqs

    Shell 13 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 409 61

  6. schard schard Public

    reticulate-free single cell format conversion

    R 126 8

Repositories

Showing 10 of 101 repositories
  • omero-download Public

    Download images from OMERO server

    cellgeni/omero-download’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Mar 3, 2025
  • 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 0 MIT 1 0 0 Updated Mar 3, 2025
  • nf-fgwas Public

    Nextflow implementation of fGWAS

    cellgeni/nf-fgwas’s past year of commit activity
    C 4 BSD-3-Clause 0 0 0 Updated Mar 3, 2025
  • 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 0 0 Updated Mar 3, 2025
  • nf-demultiplex Public

    Our Souporcell repo but for Nextflow Tower

    cellgeni/nf-demultiplex’s past year of commit activity
    Nextflow 0 MIT 0 1 0 Updated Feb 26, 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 Feb 26, 2025
  • nf-cellbender Public

    Nextflow implementation of Cellbender

    cellgeni/nf-cellbender’s past year of commit activity
    R 0 MIT 0 0 0 Updated Feb 25, 2025
  • nf-atac Public

    Pipeline to process sc-ATAC data with pyCistopic

    cellgeni/nf-atac’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Feb 25, 2025
  • nf-metacells Public
    cellgeni/nf-metacells’s past year of commit activity
    Python 0 0 0 0 Updated Feb 21, 2025
  • nf-starsolo Public

    Our STARsolo repo but designed for Nextflow Tower

    cellgeni/nf-starsolo’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Feb 21, 2025
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