Repositories list

• nf-modules

  Public

  cellgeni/nf-modules’s past year of commit activity
  Python

  •

  MIT License

  •00 forks•11 star•00 issues•22 pull requests•Updated Apr 18, 2026Apr 18, 2026

• AKOYA_analysis

  Public

  cellgeni/AKOYA_analysis’s past year of commit activity
  set of codes for analysis of sptaial proteomics datasets

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• nf-metacells

  Public

  cellgeni/nf-metacells’s past year of commit activity
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• dockage

  Public

  cellgeni/dockage’s past year of commit activity
  Cellular Genomics Informatics Dockerfiles

  Dockerfile

  •

  GNU Affero General Public License v3.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• nf-atac

  Public

  cellgeni/nf-atac’s past year of commit activity
  Pipeline to process sc-ATAC data with pyCistopic

  pythonbioinformaticspipeline+ 6

  pythonbioinformaticspipelinenextflowatac-seqsingle-cellsingle-cell-atac-seqsingle-cell-multiomicsmultiome

  Python

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• Image-ST

  Public

  cellgeni/Image-ST’s past year of commit activity
  A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode

  Python

  •

  MIT License

  •33 forks•33 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• nf-cluster

  Public

  cellgeni/nf-cluster’s past year of commit activity
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• h5ad-cli

  Public

  cellgeni/h5ad-cli’s past year of commit activity
  A CLI for operations with AnnData objects in .h5ad and .zarr files

  h5zarranndata+ 1

  h5zarranndatah5ad

  Python

  •

  MIT License

  •00 forks•66 stars•22 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• webatlas-pipeline

  Public

  cellgeni/webatlas-pipeline’s past year of commit activity
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

  Python

  •

  MIT License

  •1313 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• rapids-comparison

  Public

  cellgeni/rapids-comparison’s past year of commit activity
  Comparison of singlecell-rapids and scanpy for single-cell RNA-seq data analysis

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• alignment_HE_DAPI

  Public

  cellgeni/alignment_HE_DAPI’s past year of commit activity
  multimodal alignment H&E RGB images to DAPI one channel images

  Jupyter Notebook

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• schard

  Public

  cellgeni/schard’s past year of commit activity
  reticulate-free single cell format conversion

  R

  •

  GNU General Public License v3.0

  •1515 forks•216216 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• py8rds

  Public

  cellgeni/py8rds’s past year of commit activity
  R Data Deserialization in python

  Jupyter Notebook

  •

  MIT License

  •00 forks•1010 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• fetch-series

  Public

  cellgeni/fetch-series’s past year of commit activity
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 12, 2026Mar 12, 2026

• farmer

  Public

  cellgeni/farmer’s past year of commit activity
  Slack bot that tells you the status of your LSF jobs 🧑‍🌾

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•33 stars•22 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• nf-demultiplex

  Public

  cellgeni/nf-demultiplex’s past year of commit activity
  Our Souporcell repo but for Nextflow Tower

  Nextflow

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  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated Feb 27, 2026Feb 27, 2026

• nf-scVI-metrics

  Public

  cellgeni/nf-scVI-metrics’s past year of commit activity
  Grid search to optimise hyperparameters for scVI

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 25, 2026Feb 25, 2026

• reprocess_public_10x

  Public

  cellgeni/reprocess_public_10x’s past year of commit activity
  Scripts to help get fastqs

  Shell

  •

  GNU General Public License v3.0

  •33 forks•1919 stars•66 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• nf-scautoqc

  Public

  cellgeni/nf-scautoqc’s past year of commit activity
  Nextflow implementation of scAutoQC pipeline

  Python

  •

  GNU General Public License v3.0

  •00 forks•1111 stars•11 issue•11 pull request•Updated Feb 21, 2026Feb 21, 2026

• sceasy

  Public

  cellgeni/sceasy’s past year of commit activity
  A package to help convert different single-cell data formats to each other

  R

  •

  GNU General Public License v3.0

  •6767 forks•463463 stars•4444 issues•55 pull requests•Updated Feb 20, 2026Feb 20, 2026

• STARsolo

  Public

  cellgeni/STARsolo’s past year of commit activity
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq

  Shell

  •

  GNU General Public License v3.0

  •99 forks•8484 stars•33 issues•00 pull requests•Updated Feb 18, 2026Feb 18, 2026

• ovary

  Public

  cellgeni/ovary’s past year of commit activity
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• spatialproteomics

  Public

  cellgeni/spatialproteomics’s past year of commit activity
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly multiplexed immunohistoch…

  Python

  •

  MIT License

  •88 forks•00 stars•00 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• nf-scsajr

  Public

  cellgeni/nf-scsajr’s past year of commit activity
  single cell alternative splicing

  R

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 11, 2026Feb 11, 2026

• nf-irods-to-fastq

  Public

  cellgeni/nf-irods-to-fastq’s past year of commit activity
  Get CRAMs from iRODS and convert them to FASTQ

  Nextflow

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  MIT License

  •22 forks•22 stars•11 issue•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• xenium_velocyto

  Public

  cellgeni/xenium_velocyto’s past year of commit activity
  An attempt to use nuclear/cytoplasmic transcripts from Xenium as unspliced/spliced for velocyto

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• nf-cellbender

  Public

  cellgeni/nf-cellbender’s past year of commit activity
  Nextflow implementation of Cellbender

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 4, 2026Feb 4, 2026

• OMERO_tools

  Public

  cellgeni/OMERO_tools’s past year of commit activity
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• nf-larry

  Public

  cellgeni/nf-larry’s past year of commit activity
  Python

  •00 forks•33 stars•00 issues•00 pull requests•Updated Feb 2, 2026Feb 2, 2026

• docs

  Public

  cellgeni/docs’s past year of commit activity
  CellGen IT documentation

  docswikireadthedocs+ 1

  docswikireadthedocssanger

  MIT License

  •44 forks•11 star•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026