Repositories list

• nf-reprocessing-public-10x

  Public
  Nextflow pipeline of Alex's reprocessing scripts

  Shell

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•11 pull request•Updated May 1, 2026May 1, 2026

• dockage

  Public
  Cellular Genomics Informatics Dockerfiles

  Dockerfile

  •

  GNU Affero General Public License v3.0

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

• fetch-series

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 2026

• hdca_v2_reprocessing

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 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•33 stars•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• nf-metacells

  Public
  Python

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

• nf-cluster

  Public
  Python

  •

  MIT License

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

• nf-modules

  Public
  Python

  •

  MIT License

  •00 forks•11 star•00 issues•22 pull requests•Updated Apr 27, 2026Apr 27, 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 Apr 27, 2026Apr 27, 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 Apr 27, 2026Apr 27, 2026

• s3browser

  Public
  S3 (Ceph RGW) bucket browser

  HTML

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

• STARsolo

  Public
  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 Apr 22, 2026Apr 22, 2026

• visium_vistools

  Public
  visualisation tools for Visium outputs

  Jupyter Notebook

  •11 fork•00 stars•00 issues•11 pull request•Updated Apr 22, 2026Apr 22, 2026

• nf-scenicplus

  Public
  Nextflow

  •

  MIT License

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

• AKOYA_analysis

  Public
  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

• h5ad-cli

  Public
  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

• rapids-comparison

  Public
  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
  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
  reticulate-free single cell format conversion

  R

  •

  GNU General Public License v3.0

  •1515 forks•217217 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• py8rds

  Public
  R Data Deserialization in python

  Jupyter Notebook

  •

  MIT License

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

• farmer

  Public
  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
  Our Souporcell repo but for Nextflow Tower

  Nextflow

  •

  MIT License

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

• nf-scVI-metrics

  Public
  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
  Scripts to help get fastqs

  Shell

  •

  GNU General Public License v3.0

  •33 forks•1919 stars•77 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• nf-scautoqc

  Public
  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
  A package to help convert different single-cell data formats to each other

  R

  •

  GNU General Public License v3.0

  •6767 forks•465465 stars•4444 issues•55 pull requests•Updated Feb 20, 2026Feb 20, 2026

• ovary

  Public
  Jupyter Notebook

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

• spatialproteomics

  Public
  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
  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
  Get CRAMs from iRODS and convert them to FASTQ

  Nextflow

  •

  MIT License

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