Repositories list

• SPiCe

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Feb 1, 2026Feb 1, 2026

• EMP-FM

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•4•0•0•Updated Jan 2, 2026Jan 2, 2026

• secrierlab.github.io

  Public
  The Secrier lab website.

  HTML

  •0•0•0•0•Updated Dec 20, 2025Dec 20, 2025

• EnrichMap

  Public
  EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics.

  geneset-enrichmentspatial-transcriptomics

  Python

  •

  GNU General Public License v3.0

  •4•13•1•0•Updated Dec 11, 2025Dec 11, 2025

• Metastatic-melanoma-anti-PD1

  Public
  Analysis of metastatic melanoma anti-PD1 dataset from Li et al

  R

  •0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• enrichmap-reproducibility

  Public
  Reproducibility repository for EnrichMap preprint.

  Jupyter Notebook

  •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• G0-FM

  Public
  A foundation model to classify G0, slow and fast cycling states in single cell RNA-seq cancer data. This model has currently been trained on breast cancer only.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Mar 3, 2025Mar 3, 2025

• G0-breast-cancer-atlas

  Public
  G0 breast cancer atlas

  quiescencebreast-cancersingle-cell-rna-seq+ 2spatial-transcriptomicsg0-arrest

  R

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Feb 12, 2025Feb 12, 2025

• SpottedPy

  Public
  Hotspot cluster distance analysis in spatial transcriptomic data

  clusterspatialtranscriptomics+ 3hotspotsdistanceshotspots-analysis

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•35•1•0•Updated Feb 10, 2025Feb 10, 2025

• CancerG0Arrest

  Public
  Evaluation of cell cycle arrest from transcriptomics data.

  cancerquiescencemulti-omics+ 1dormancy

  R

  •

  GNU General Public License v3.0

  •1•4•1•0•Updated Jun 26, 2024Jun 26, 2024

• HistoMIL

  Public
  A Python package for handling histopathology whole-slide images using multiple instance learning (MIL) techniques.

  deep-learninghistopathology-image-analysis

  Python

  •

  GNU General Public License v3.0

  •8•29•0•2•Updated May 21, 2024May 21, 2024

• MultiscaleHRD

  Public
  R

  •

  GNU General Public License v3.0

  •0•1•2•0•Updated Feb 23, 2024Feb 23, 2024

• IDH_mutant_glioma_subtypes

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 19, 2024Feb 19, 2024

• HNSCC-immunity-landscape

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 3, 2023Jul 3, 2023

• Mutational-Signatures-OAC

  Public
  Analysis of mutational signature dynamics across stages of oesophageal adenocarcinoma development.

  R

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Jun 21, 2023Jun 21, 2023

• MouseSARSCov2Infection

  Public
  R

  •0•0•0•0•Updated Mar 9, 2023Mar 9, 2023

• EMT

  Public
  This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.

  cancerbulksingle-cell+ 1emt

  R

  •3•13•1•0•Updated Jan 24, 2023Jan 24, 2023

• TumourHistologyDL

  Public
  Characteraising the immunological landscape and spatial architecture of colon cancer tissue

  Jupyter Notebook

  •

  MIT License

  •0•2•1•0•Updated Feb 25, 2022Feb 25, 2022

• tumourMassDormancy

  Public
  This repository contains the code developed for the analysis of tumour mass dormancy, immunological and angiogenic dormancy across cancers from the Cancer Genom…

  cancerdormancybulk-sequencing

  R

  •

  GNU General Public License v3.0

  •1•5•0•0•Updated Apr 20, 2021Apr 20, 2021