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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 69 8

  2. reprocess_public_10x reprocess_public_10x Public

    Scripts to help get fastqs

    Shell 14 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 444 65

  6. schard schard Public

    reticulate-free single cell format conversion

    R 191 11

Repositories

Showing 10 of 126 repositories
  • nf-upload2irods Public

    Pipeline for uploading files to iRODS system

    cellgeni/nf-upload2irods’s past year of commit activity
    Nextflow 0 MIT 1 0 0 Updated Oct 23, 2025
  • xenium_velocyto Public

    An attempt to use nuclear/cytoplasmic transcripts from Xenium as unspliced/spliced for velocyto

    cellgeni/xenium_velocyto’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 23, 2025
  • bulk_rnaseq Public

    Wrapper scripts for convenient processing of bulk RNA-seq experiments

    cellgeni/bulk_rnaseq’s past year of commit activity
    Shell 1 GPL-3.0 0 0 0 Updated Oct 22, 2025
  • nf-cellbender Public

    Nextflow implementation of Cellbender

    cellgeni/nf-cellbender’s past year of commit activity
    R 0 MIT 0 0 0 Updated Oct 16, 2025
  • dockage Public

    Cellgeni Docker files

    cellgeni/dockage’s past year of commit activity
    Dockerfile 3 AGPL-3.0 0 0 0 Updated Oct 15, 2025
  • nf-metacells Public
    cellgeni/nf-metacells’s past year of commit activity
    Python 0 0 0 0 Updated Oct 15, 2025
  • nf-processed2irods Public

    Pipeline to move processed datasets to irods

    cellgeni/nf-processed2irods’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 14, 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 Oct 14, 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 2 MIT 2 0 0 Updated Oct 8, 2025
  • reprocess_public_10x Public

    Scripts to help get fastqs

    cellgeni/reprocess_public_10x’s past year of commit activity
    Shell 14 GPL-3.0 3 2 0 Updated Oct 7, 2025
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