Repositories list

• ClassyFlow

  Public
  In Development nextflow workflow specific to outlining approaches to building and testing ML classifiers

  Python

  •

  MIT License

  •00 forks•00 stars•44 issues•00 pull requests•Updated Sep 2, 2026Sep 2, 2026

• MultimodalityHistoComb

  Public
  Combining multimodality histopathology images for integrated cancer research

  multimodalitydataintegration

  multimodalitydataintegration

  Jupyter Notebook

  •

  MIT License

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

• Languages-of-Omics

  Public
  Can AI Become Biology's Universal Translator?

  Python

  •

  MIT License

  •11 fork•44 stars•00 issues•00 pull requests•Updated Aug 25, 2026Aug 25, 2026

• BinFlow

  Public
  The NextFlow pipeline that will calculated multiple individual binary markers

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 5, 2026Aug 5, 2026

• open-model-explorer

  Public
  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2026Jul 30, 2026

• MorphoSpectrum-MIL

  Public
  MorphoXAI: A human-in-the-loop explanation framework for morphologically transparent AI predictions from whole-slide images

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated May 31, 2026May 31, 2026

• StereoAnalysis

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• OLT-Alloimmunity

  Public
  Processed data storage for "Spatial multiomics of human hepatic lymph nodes reveals early APC bifurcation in liver transplant rejection"

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 15, 2026Mar 15, 2026

• TMA_Graph_Embedding

  Public
  Jupyter Notebook

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

• qupath-extension-cloud-omezarr

  Public
  QuPath extension to load OME-Zarr images from cloud storage

  Kotlin

  •

  GNU General Public License v3.0

  •00 forks•22 stars•88 issues•00 pull requests•Updated Dec 28, 2025Dec 28, 2025

• AnnotationStreamlit

  Public
  Python

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

• DicomToSVS

  Public
  Jupyter Notebook

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

• TIL-SIL-Detection

  Public
  Jupyter Notebook

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

• SpaFlow

  Public
  A Nextflow pipeline for QC and unsupervised clustering of spatial biology data

  Nextflow

  •

  MIT License

  •11 fork•1515 stars•00 issues•00 pull requests•Updated Nov 4, 2025Nov 4, 2025

• GSEA_custom

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 8, 2025Oct 8, 2025

• StereoSeq

  Public
  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Sep 19, 2025Sep 19, 2025

• DeconvolutionWF

  Public
  Python

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

• TMA_Alignment

  Public
  This project is for alignment between H&E-stained whole slide image and multiplex immunofluorescence images.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 12, 2025Aug 12, 2025

• Sherman_Cancer_DCIS_Segmentation

  Public
  DCIS and Invasive Cancer Detection Code for Breast Cancer (Sherman Project)

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 3, 2025Aug 3, 2025

• TRADER

  Public
  CIM app for rare disease drug query

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2025Jul 30, 2025

• sherman_lab

  Public
  Code repo for the Sherman lab

  00 forks•00 stars•00 issues•00 pull requests•Updated Jul 25, 2025Jul 25, 2025

• dimi-lab.github.io

  Public template
  Data science and Informatics for Multiomics Integration

  data-sciencebioinformaticsdataanalysis+ 2

  data-sciencebioinformaticsdataanalysismultiomicsspatialomics

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •33 forks•00 stars•00 issues•22 pull requests•Updated Jun 25, 2025Jun 25, 2025

• Scalable_Labelled_SegMasks_To_QuPath

  Public
  Small nextflow pipeline to be able to take external SegMask files and load into QuPath (100k+ Segments)

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated May 4, 2025May 4, 2025

• deepCSeq_evaluation

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2025Mar 28, 2025

• drpllm

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 14, 2025Mar 14, 2025

• PPAR

  Public
  The Rank order prediction of genes for a given set of phenotypes for mendelian and rare disease framework (RPAR)

  Jupyter Notebook

  •

  MIT License

  •00 forks•99 stars•00 issues•00 pull requests•Updated Feb 19, 2025Feb 19, 2025

• SCdeconR

  Public
  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 20, 2024Dec 20, 2024

• The_Handy_OMERO_Toolbox

  Public
  An assortment of scripts used to interface with our internal instance of OMERO and accomplish custom tasks

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Oct 11, 2024Oct 11, 2024

• TumorStromaReaction

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 30, 2024Sep 30, 2024

• Collab_Bartemes_OPSCC

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 19, 2024Jul 19, 2024