Repositories list

• OMERO_tools

  Public
  Python

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

• nf-modules

  Public
  Python

  •

  MIT License

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

• explorer

  Public
  TypeScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• dockage

  Public
  Cellular Genomics Informatics Dockerfiles

  Dockerfile

  •

  GNU Affero General Public License v3.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• nf-processed2irods

  Public
  Pipeline to move processed datasets to irods

  Nextflow

  •

  MIT License

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

• STARsolo

  Public
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq

  Shell

  •

  GNU General Public License v3.0

  •99 forks•9292 stars•33 issues•00 pull requests•Updated Jul 16, 2026Jul 16, 2026

• pidgeon

  Public
  registration package

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 14, 2026Jul 14, 2026

• nf-metacells

  Public
  Python

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

• schard

  Public
  reticulate-free single cell format conversion

  R

  •

  GNU General Public License v3.0

  •1717 forks•219219 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• nf-scautoqc

  Public
  Nextflow implementation of scAutoQC pipeline

  Python

  •

  GNU General Public License v3.0

  •00 forks•1212 stars•11 issue•11 pull request•Updated Jul 9, 2026Jul 9, 2026

• nf-reprocessing-public-10x

  Public
  Nextflow pipeline of Alex's reprocessing scripts

  Shell

  •

  GNU General Public License v3.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jul 2, 2026Jul 2, 2026

• nf-autoannotate

  Public
  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 1, 2026Jul 1, 2026

• nf-cellbender

  Public
  Nextflow implementation of Cellbender

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 30, 2026Jun 30, 2026

• nf-upload2irods

  Public
  Pipeline for uploading files to iRODS system

  Nextflow

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 29, 2026Jun 29, 2026

• visium_vistools

  Public
  visualisation tools for Visium outputs

  Jupyter Notebook

  •11 fork•00 stars•00 issues•11 pull request•Updated Jun 23, 2026Jun 23, 2026

• webatlas-pipeline

  Public
  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 Jun 23, 2026Jun 23, 2026

• bsubs

  Public
  LSF Submission examples

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 23, 2026Jun 23, 2026

• iranger

  Public
  Read 10x analysis from iRODS

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jun 18, 2026Jun 18, 2026

• compare-peaks

  Public
  Compare different peak calling approaches

  Jupyter Notebook

  •

  MIT License

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

• alignment_HE_DAPI

  Public
  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 Jun 4, 2026Jun 4, 2026

• Image-ST

  Public
  A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode

  Python

  •

  MIT License

  •33 forks•55 stars•00 issues•00 pull requests•Updated Jun 1, 2026Jun 1, 2026

• nf-atac

  Public
  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 May 23, 2026May 23, 2026

• py8rds

  Public
  R Data Deserialization in python

  Jupyter Notebook

  •

  MIT License

  •00 forks•1414 stars•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• docs

  Public
  CellGen IT documentation

  docswikireadthedocs+ 1

  docswikireadthedocssanger

  MIT License

  •44 forks•11 star•00 issues•00 pull requests•Updated May 14, 2026May 14, 2026

• reprocess_public_10x

  Public
  Scripts to help get fastqs

  Shell

  •

  GNU General Public License v3.0

  •33 forks•1919 stars•77 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• fetch-series

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• fce

  Public
  Get OpenStack instance IPs from the command line.

  Python

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

• fastapi_websocket_rpc

  Public
  ⚡ FASTAPI Websocket RPC- A fast and durable bidirectional JSON RPC channel over Websockets.

  Python

  •

  MIT License

  •3333 forks•11 star•00 issues•00 pull requests•Updated May 11, 2026May 11, 2026

• AKOYA_analysis

  Public
  set of codes for analysis of sptaial proteomics datasets

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated May 5, 2026May 5, 2026

• nf-cluster

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026