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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 64 7

  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 438 65

  6. schard schard Public

    reticulate-free single cell format conversion

    R 183 11

Repositories

Showing 10 of 122 repositories
  • 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 9, 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
  • nf-modules Public
    cellgeni/nf-modules’s past year of commit activity
    Python 1 MIT 0 0 1 Updated Sep 5, 2025
  • spatialxe Public Forked from nf-core/spatialxe
    cellgeni/spatialxe’s past year of commit activity
    Nextflow 0 MIT 9 0 0 Updated Sep 5, 2025
  • watergate Public

    Wiretaps for things

    cellgeni/watergate’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 4, 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 3, 2025
  • nf-irods-to-fastq Public

    Get CRAMs from iRODS and convert them to FASTQ

    cellgeni/nf-irods-to-fastq’s past year of commit activity
    Nextflow 2 MIT 2 1 0 Updated Sep 1, 2025
  • dockage Public

    Cellgeni Docker files

    cellgeni/dockage’s past year of commit activity
    Dockerfile 3 AGPL-3.0 0 0 0 Updated Aug 28, 2025
  • nf-c2l Public
    cellgeni/nf-c2l’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Aug 27, 2025
  • 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 Aug 26, 2025
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