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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 128 8

Repositories

Showing 10 of 102 repositories
  • nf-scVI-metrics Public

    Grid search to optimise hyperparameters for scVI

    cellgeni/nf-scVI-metrics’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Mar 7, 2025
  • docs Public

    CellGen IT documentation

    cellgeni/docs’s past year of commit activity
    1 MIT 4 0 0 Updated Mar 7, 2025
  • dockage Public

    Cellgeni Docker files

    cellgeni/dockage’s past year of commit activity
    Dockerfile 1 AGPL-3.0 0 0 0 Updated Mar 7, 2025
  • nf-scautoqc Public

    Nextflow implementation of scAutoQC pipeline

    cellgeni/nf-scautoqc’s past year of commit activity
    Python 3 GPL-3.0 0 0 0 Updated Mar 6, 2025
  • 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 5, 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 1 MIT 1 0 0 Updated Mar 4, 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 4, 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
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