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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 93 10

  2. reprocess_public_10x reprocess_public_10x Public

    Scripts to help get fastqs

    Shell 19 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 220 16

Repositories

Showing 10 of 146 repositories
  • fetch-series Public
    cellgeni/fetch-series's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 1 Updated Sep 16, 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 0 0 0 Updated Sep 16, 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 7 MIT 0 1 0 Updated Sep 15, 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 1 0 Updated Sep 14, 2026
  • c2l Public

    Set of scripts to run cell2location on farm

    cellgeni/c2l's past year of commit activity
    Jupyter Notebook 2 MIT 0 0 0 Updated Sep 9, 2026
  • dockage Public

    Cellular Genomics Informatics Dockerfiles

    cellgeni/dockage's past year of commit activity
    Dockerfile 3 AGPL-3.0 1 0 0 Updated Sep 9, 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 8, 2026
  • validate-hierarchy Public

    Validate directory and iRODS collection hierarchies against a declarative YAML schema

    cellgeni/validate-hierarchy's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 8, 2026
  • nf-modules Public
    cellgeni/nf-modules's past year of commit activity
    Python 1 MIT 0 0 2 Updated Sep 7, 2026
  • nf-scsajr Public

    single cell alternative splicing

    cellgeni/nf-scsajr's past year of commit activity
    R 2 0 0 0 Updated Sep 4, 2026
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