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    28 repositories

    • webatlas-pipeline

      Public
      A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
      rse
      rse
      Python
      •
      MIT License
      •13•68•15•6•Updated Apr 24, 2026Apr 24, 2026

    • cherita-react

      Public
      A React component library designed for data visualisation and analysis of single-cell and spatial multi-omics data
      rse
      rse
      JavaScript
      •
      MIT License
      •0•0•19•5•Updated Apr 24, 2026Apr 24, 2026

    • cherita-flask-api

      Public
      A web service designed to provide a robust and scalable interface for managing and analyzing biological data
      rse
      rse
      Python
      •
      MIT License
      •0•0•6•8•Updated Apr 14, 2026Apr 14, 2026

    • solosis

      Public
      A plug and play CLI for the lab
      rse
      rse
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•5•7•Updated Mar 30, 2026Mar 30, 2026

    • scanpy_plus

      Public
      Minion functions to make life with scanpy easier
      Jupyter Notebook
      •
      MIT License
      •1•0•2•1•Updated Mar 19, 2026Mar 19, 2026

    • hlbfx_project

      Public
      Project creation suite for Haniffa lab
      Shell
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Mar 18, 2026Mar 18, 2026

    • strapi-api

      Public
      A backend API powered by Strapi, designed to manage and serve content within the Cherita infrastructure
      rse
      rse
      JavaScript
      •
      MIT License
      •0•0•2•2•Updated Mar 2, 2026Mar 2, 2026

    • cns-haematopoiesis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 6, 2026Feb 6, 2026

    • spatial_skin_atlas

      Public
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 13, 2026Jan 13, 2026

    • skin_fibroblast_atlas

      Public
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •3•18•0•0•Updated Jan 11, 2026Jan 11, 2026

    • webatlas-app

      Public
      An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.
      rse
      rse
      JavaScript
      •
      MIT License
      •4•15•3•2•Updated Nov 3, 2025Nov 3, 2025

    • scanpy_bioinfoteam

      Public
      Single-cell analysis in Python. Scales to >100M cells.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •741•0•0•1•Updated May 9, 2025May 9, 2025

    • data_managment

      Public
      0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • adifa

      Public archive
      Adifa is a framework for visualising single-cell gene expression data in a web browser.
      rse
      rse
      JavaScript
      •
      MIT License
      •2•2•0•0•Updated Dec 19, 2024Dec 19, 2024

    • haniffalab.github.io

      Public
      rse
      rse
      HTML
      •3•1•1•0•Updated Dec 16, 2024Dec 16, 2024

    • CTCL_NatureImmunology

      Public
      Single-cell RNA sequencing study of Cutaneous T cell lymphoma
      Jupyter Notebook
      •3•0•0•0•Updated Oct 20, 2024Oct 20, 2024

    • FCA_fetal_skin

      Public
      This repository contains the data processing and analysis scripts for fetal skin study.
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •3•5•0•0•Updated Sep 13, 2024Sep 13, 2024

    • scENTInEL

      Public
      Scentinel is a probabilistic ensemble framework designed for mapping large single-cell (sc) multi-omic datasets using either transductive or inductive transfer …
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•1•1•Updated Sep 6, 2024Sep 6, 2024

    • FCA_yolkSac

      Public
      Repository containing all code for HCA yolk sac analysis
      Jupyter Notebook
      •
      Other
      •3•5•0•0•Updated Jul 13, 2023Jul 13, 2023

    • vitessce

      Public
      Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
      rse
      rse
      JavaScript
      •
      MIT License
      •59•0•0•0•Updated May 18, 2022May 18, 2022

    • Single-cell-RNAseq-data-analysis-bundle

      Public
      R
      •
      MIT License
      •10•12•0•0•Updated May 4, 2022May 4, 2022

    • FCA_bone_marrow

      Public
      This repository contains all analysis scripts used to explore single cell datasets for: Jardine and Webb et al., 2021, "Blood and immune development in human fe…
      Jupyter Notebook
      •
      MIT License
      •6•13•0•0•Updated May 4, 2022May 4, 2022

    • HL_open_source_hardware

      Public
      Open source repository for hardware and associated software developed within the Haniffalab
      G-code
      •
      MIT License
      •1•1•0•0•Updated May 4, 2022May 4, 2022

    • covid_nasal_epithelium

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Sep 3, 2021Sep 3, 2021

    • HCA_skin

      Public
      HCA data analysis
      Jupyter Notebook
      •3•19•2•0•Updated Mar 30, 2021Mar 30, 2021

    • SCC_project

      Public
      SCC project scripts
      0•0•0•0•Updated Feb 8, 2021Feb 8, 2021

    • FCA_liver

      Public
      All software used for “Decoding human fetal liver haematopoiesis” (Popescu, Botting, Stephenson et al., 2019).
      R
      •16•39•0•0•Updated May 15, 2020May 15, 2020

    • scRNA-seq_analysis

      Public
      Single cell RNA-seq analysis bundle
      R
      •11•37•0•0•Updated Sep 13, 2019Sep 13, 2019
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