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@haniffalab

Haniffa Lab

Based in the Newcastle University Biosciences Institute, we apply disruptive techniques to understand how the immune system develops and maintains health

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  1. webatlas-pipeline webatlas-pipeline Public

    A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

    Python 44 9

  2. FCA_liver FCA_liver Public

    All software used for “Decoding human fetal liver haematopoiesis” (Popescu, Botting, Stephenson et al., 2019).

    R 38 16

  3. scRNA-seq_analysis scRNA-seq_analysis Public

    Single cell RNA-seq analysis bundle

    R 33 10

  4. HCA_skin HCA_skin Public

    HCA data analysis

    Jupyter Notebook 15 3

  5. FCA_bone_marrow 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 fetal bone marrow and in Down syndrome"…

    Jupyter Notebook 14 6

  6. webatlas-app webatlas-app Public

    An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.

    JavaScript 13 3

Repositories

Showing 10 of 27 repositories
  • webatlas-pipeline Public

    A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

    haniffalab/webatlas-pipeline’s past year of commit activity
    Python 44 MIT 9 11 (1 issue needs help) 4 Updated Nov 18, 2024
  • jekyll-cellatlas-io-collections Public
    haniffalab/jekyll-cellatlas-io-collections’s past year of commit activity
    CSS 0 1 0 0 Updated Nov 14, 2024
  • solosis Public

    A plug and play pipeline for the lab

    haniffalab/solosis’s past year of commit activity
    Jupyter Notebook 0 GPL-3.0 0 12 (2 issues need help) 2 Updated Nov 13, 2024
  • jekyll-hdca Public
    haniffalab/jekyll-hdca’s past year of commit activity
    CSS 0 0 9 0 Updated Nov 12, 2024
  • strapi-api Public
    haniffalab/strapi-api’s past year of commit activity
    JavaScript 0 0 0 1 Updated Oct 16, 2024
  • sci-adifa Public
    haniffalab/sci-adifa’s past year of commit activity
    JavaScript 2 MIT 2 6 0 Updated Sep 13, 2024
  • FCA_fetal_skin Public

    This repository contains the data processing and analysis scripts for fetal skin study.

    haniffalab/FCA_fetal_skin’s past year of commit activity
    Jupyter Notebook 3 AGPL-3.0 1 0 0 Updated Sep 13, 2024
  • haniffalab.github.io Public
    haniffalab/haniffalab.github.io’s past year of commit activity
    HTML 0 2 6 0 Updated Sep 6, 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 learning. The framework operates on pre-integrated low-dimensional latent embeddings and offers multiple algorithmic modalities.

    haniffalab/scENTInEL’s past year of commit activity
    Jupyter Notebook 3 BSD-3-Clause 3 1 1 Updated Sep 6, 2024
  • sc-analysis-nf Public

    pipeline to

    haniffalab/sc-analysis-nf’s past year of commit activity
    Python 0 0 1 0 Updated Mar 12, 2024
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