Repositories list

• SPiCe

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 3, 2026Aug 3, 2026

• G0-breast-cancer-atlas

  Public
  G0 breast cancer atlas

  quiescencebreast-cancersingle-cell-rna-seq+ 2

  quiescencebreast-cancersingle-cell-rna-seqspatial-transcriptomicsg0-arrest

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •22 forks•33 stars•00 issues•00 pull requests•Updated Jun 29, 2026Jun 29, 2026

• EnrichMap

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

  geneset-enrichmentspatial-transcriptomics

  geneset-enrichmentspatial-transcriptomics

  Python

  •

  GNU General Public License v3.0

  •44 forks•1717 stars•11 issue•00 pull requests•Updated Jun 26, 2026Jun 26, 2026

• enrichmap-reproducibility

  Public
  Reproducibility repository for EnrichMap preprint.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 25, 2026Jun 25, 2026

• EMP-FM

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •22 forks•66 stars•00 issues•00 pull requests•Updated Jan 2, 2026Jan 2, 2026

• secrierlab.github.io

  Public
  The Secrier lab website.

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 20, 2025Dec 20, 2025

• Metastatic-melanoma-anti-PD1

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

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 11, 2025Aug 11, 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

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 3, 2025Mar 3, 2025

• SpottedPy

  Public
  Hotspot cluster distance analysis in spatial transcriptomic data

  clusterspatialtranscriptomics+ 3

  clusterspatialtranscriptomicshotspotsdistanceshotspots-analysis

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•3737 stars•11 issue•00 pull requests•Updated Feb 10, 2025Feb 10, 2025

• CancerG0Arrest

  Public
  Evaluation of cell cycle arrest from transcriptomics data.

  cancerquiescencemulti-omics+ 1

  cancerquiescencemulti-omicsdormancy

  R

  •

  GNU General Public License v3.0

  •11 fork•44 stars•11 issue•00 pull requests•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

  deep-learninghistopathology-image-analysis

  Python

  •

  GNU General Public License v3.0

  •99 forks•3030 stars•00 issues•22 pull requests•Updated May 21, 2024May 21, 2024

• MultiscaleHRD

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•11 star•22 issues•00 pull requests•Updated Feb 23, 2024Feb 23, 2024

• IDH_mutant_glioma_subtypes

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 19, 2024Feb 19, 2024

• HNSCC-immunity-landscape

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jun 21, 2023Jun 21, 2023

• MouseSARSCov2Infection

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•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+ 1

  cancerbulksingle-cellemt

  R

  •33 forks•1313 stars•11 issue•00 pull requests•Updated Jan 24, 2023Jan 24, 2023

• TumourHistologyDL

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

  Jupyter Notebook

  •

  MIT License

  •00 forks•22 stars•11 issue•00 pull requests•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

  cancerdormancybulk-sequencing

  R

  •

  GNU General Public License v3.0

  •11 fork•55 stars•00 issues•00 pull requests•Updated Apr 20, 2021Apr 20, 2021