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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 48 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 401 59

  6. schard schard Public

    reticulate-free single cell format conversion

    R 111 6

Repositories

Showing 10 of 97 repositories
  • nf-scsajr Public

    single cell alternative splicing

    cellgeni/nf-scsajr’s past year of commit activity
    R 0 0 0 0 Updated Jan 23, 2025
  • nf-cellbender Public

    Nextflow implementation of Cellbender

    cellgeni/nf-cellbender’s past year of commit activity
    R 0 MIT 0 0 0 Updated Jan 23, 2025
  • alignment_HE_DAPI Public

    multimodal alignment H&E RGB images to DAPI one channel images

    cellgeni/alignment_HE_DAPI’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jan 23, 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 Jan 23, 2025
  • nf-fgwas Public

    Nextflow implementation of fGWAS

    cellgeni/nf-fgwas’s past year of commit activity
    C 3 BSD-3-Clause 0 0 0 Updated Jan 22, 2025
  • reprocess_public_10x Public

    Scripts to help get fastqs

    cellgeni/reprocess_public_10x’s past year of commit activity
    Shell 13 GPL-3.0 3 0 1 Updated Jan 21, 2025
  • visutils Public

    set of function for qc and visualization of Visium data

    cellgeni/visutils’s past year of commit activity
    R 2 MIT 0 0 0 Updated Jan 13, 2025
  • cloupe Public

    Cloupe reader

    cellgeni/cloupe’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Jan 13, 2025
  • nf-atac Public

    Pipeline to process sc-ATAC data with pyCistopic

    cellgeni/nf-atac’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 10, 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 Jan 9, 2025
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