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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 66 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 441 65

  6. schard schard Public

    reticulate-free single cell format conversion

    R 186 11

Repositories

Showing 10 of 125 repositories
  • ticket-3970 Public

    Scripts for integration of Xenium datasets

    cellgeni/ticket-3970’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 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 1 0 Updated Sep 25, 2025
  • nf-reprocessing-public-10x Public

    Nextflow pipeline of Alex's reprocessing scripts

    cellgeni/nf-reprocessing-public-10x’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Sep 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

    cellgeni/cells2visium’s past year of commit activity
    Python 1 MIT 1 0 0 Updated Sep 24, 2025
  • Spatial_Hackathon_2025 Public

    Genome Campus Spatial Hackathon

    cellgeni/Spatial_Hackathon_2025’s past year of commit activity
    Python 0 1 0 2 Updated Sep 24, 2025
  • dockage Public

    Cellgeni Docker files

    cellgeni/dockage’s past year of commit activity
    Dockerfile 3 AGPL-3.0 0 0 0 Updated Sep 22, 2025
  • schard Public

    reticulate-free single cell format conversion

    cellgeni/schard’s past year of commit activity
    R 186 GPL-3.0 11 1 0 Updated Sep 22, 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 Sep 19, 2025
  • nf-larry Public
    cellgeni/nf-larry’s past year of commit activity
    Python 1 0 0 0 Updated Sep 15, 2025
  • scsajr Public

    R package for nf-scsajr

    cellgeni/scsajr’s past year of commit activity
    HTML 2 0 0 0 Updated Sep 9, 2025
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