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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 95 10

  2. reprocess_public_10x reprocess_public_10x Public

    Scripts to help get fastqs

    Shell 20 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 470 69

  6. schard schard Public

    reticulate-free single cell format conversion

    R 221 16

Repositories

Showing 10 of 147 repositories
  • docs Public

    CellGen IT documentation

    cellgeni/docs's past year of commit activity
    1 MIT 4 0 1 Updated Oct 7, 2026
  • nf-reprocessing-public-10x Public

    A pipeline to reprocess public 10X scRNA-seq datasets

    cellgeni/nf-reprocessing-public-10x's past year of commit activity
    Python 0 GPL-3.0 0 24 0 Updated Oct 6, 2026
  • nf-demultiplex-matfet Public

    Nextflow pipeline that separates maternal and fetal cells in single-cell RNA-seq by genotype.

    cellgeni/nf-demultiplex-matfet's past year of commit activity
    Python 0 0 0 0 Updated Oct 6, 2026
  • 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 Oct 6, 2026
  • py8rds Public

    R Data Deserialization in python

    cellgeni/py8rds's past year of commit activity
    Jupyter Notebook 15 MIT 0 0 0 Updated Sep 30, 2026
  • nf-scautoqc Public

    Nextflow implementation of scAutoQC pipeline

    cellgeni/nf-scautoqc's past year of commit activity
    Python 12 GPL-3.0 0 1 1 Updated Sep 30, 2026
  • adata-cli Public

    A CLI for operations with AnnData objects in .h5ad and .zarr files

    cellgeni/adata-cli's past year of commit activity
    Python 8 MIT 0 13 0 Updated Sep 24, 2026
  • 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 5 MIT 3 0 0 Updated Sep 21, 2026
  • 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 Sep 17, 2026
  • cell_matcher Public

    Match cells between segmentation outputs from the same sample

    cellgeni/cell_matcher's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Sep 17, 2026
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