Repositories list

• qupath-annotation-alignment

  Public
  QuPath scripts for alignment and transfer of slide annotations from one image to another

  Groovy

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 2, 2026Jun 2, 2026

• qupath-extension-ndpa-keep-colors

  Public
  Reader / Writer for Hamamatsu NDPA annotation files

  Java

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 2, 2026Jun 2, 2026

• AWS-LOGIN-SOP

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• qupath-extension-align-HE-IF

  Public
  Fork of QuPath extension to interactively align H&E and mIF images

  Java

  •

  GNU General Public License v3.0

  •1010 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2025Aug 7, 2025

• Bashore_aneurysm

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 21, 2025Apr 21, 2025

• visium_analysis

  Public
  Python

  •

  MIT License

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

• LuminexTools

  Public
  Luminex related processing pipeline

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 28, 2024Jun 28, 2024

• OlinkApp

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 17, 2024Jun 17, 2024

• visium_segmentation

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 22, 2024Feb 22, 2024

• visium_deconvolution

  Public
  Batchfile

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 22, 2024Feb 22, 2024

• clustergrammer-gl

  Public
  WebGL Clustergrammer JavaScript Library

  webglbiologyheatmap+ 2

  webglbiologyheatmapreglhacktoberfest

  JavaScript

  •

  MIT License

  •1818 forks•2323 stars•2626 issues•1414 pull requests•Updated Aug 21, 2023Aug 21, 2023

• visium-clustergrammer2

  Public
  Spatial Transcriptomics Dashboard

  pythonwebgljupyter+ 4

  pythonwebgljupyterheatmapscrna-seqvoilavisium

  Jupyter Notebook

  •

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

  •55 forks•2727 stars•1111 issues•11 pull request•Updated Jul 6, 2023Jul 6, 2023

• codex_dashboard

  Public
  Single Cell Multiplexed Imaging Jupyter Voila Dashboard using CODEX Data

  Jupyter Notebook

  •

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

  •44 forks•1717 stars•55 issues•11 pull request•Updated Jul 6, 2023Jul 6, 2023

• himc_dockers

  Public
  Docker builds for all tools used by HIMC

  Dockerfile

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 17, 2023Mar 17, 2023

• clustergrammer-widget2-deprecated

  Public
  Python

  •

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

  •00 forks•00 stars•00 issues•2525 pull requests•Updated Jan 4, 2023Jan 4, 2023

• clustergrammer2

  Public
  "Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

  visualizationjavascriptpython+ 8

  visualizationjavascriptpythonwebglbinderbiologyheatmapreglhacktoberfestjupyter-widgets+ 1

  HTML

  •

  MIT License

  •2020 forks•120120 stars•2929 issues•2727 pull requests•Updated Dec 30, 2022Dec 30, 2022

• cytutils

  Public
  Cytometry quality control and reproducibility utilities

  R

  •

  GNU General Public License v3.0

  •77 forks•88 stars•22 issues•11 pull request•Updated Aug 23, 2022Aug 23, 2022

• VEGF_A_Hormigo

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jun 22, 2022Jun 22, 2022

• LuminexApp

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 18, 2022Mar 18, 2022

• recursive_gsea

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 9, 2021Dec 9, 2021

• clustergrammer2-notebooks

  Public
  Examples using Clustergrammer2 to explore high-dimensional datasets.

  bioinformaticsbinderjupyter+ 3

  bioinformaticsbinderjupyternotebookscrna-seqbinder-ready

  Jupyter Notebook

  •1111 forks•4040 stars•88 issues•00 pull requests•Updated Aug 24, 2020Aug 24, 2020

• covid-19_sinai_reviews

  Public
  Jupyter Notebook

  •

  Other

  •77 forks•88 stars•11 issue•22 pull requests•Updated Jul 31, 2020Jul 31, 2020

• biomed-scientist-against-visa-bans

  Public
  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 13, 2020Jul 13, 2020

• rapids-single-cell-examples

  Public
  Examples of single-cell genomic analysis accelerated with RAPIDS

  Jupyter Notebook

  •

  Apache License 2.0

  •6969 forks•11 star•00 issues•00 pull requests•Updated May 29, 2020May 29, 2020

• covid-19_tenoever

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2020Apr 27, 2020

• LegendScreen_CyTOF

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 21, 2020Apr 21, 2020

• himc_helper_functions

  Public
  Python

  •00 forks•00 stars•88 issues•00 pull requests•Updated Feb 22, 2020Feb 22, 2020

• clustergrammer2-signatures

  Public
  Collection of cell type and cell state signatures built to easily integrate with Clustergrammer2 single cell toolkit.

  00 forks•00 stars•11 issue•00 pull requests•Updated Feb 9, 2020Feb 9, 2020

• clustergrammer2-test

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 10, 2019Nov 10, 2019

• cellranger-aws-pipeline-docs

  Public
  Python

  •22 forks•11 star•00 issues•11 pull request•Updated Sep 25, 2019Sep 25, 2019