Repositories list

• SPACEc

  Public
  Jupyter Notebook

  •

  Other

  •1919 forks•1717 stars•00 issues•00 pull requests•Updated Sep 19, 2025Sep 19, 2025

• NeighborhoodCoordination

  Public
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"

  Jupyter Notebook

  •2020 forks•7171 stars•22 issues•00 pull requests•Updated Nov 4, 2024Nov 4, 2024

• cytof-backer-upper

  Public
  Script for backing up CyTOF data to Google cloud storage

  Python

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jul 19, 2024Jul 19, 2024

• citrus

  Public
  Citrus Development Code

  R

  •

  GNU General Public License v3.0

  •2020 forks•3131 stars•4646 issues•00 pull requests•Updated Apr 14, 2024Apr 14, 2024

• REDSEA

  Public
  Jupyter Notebook

  •

  Other

  •1111 forks•1818 stars•00 issues•00 pull requests•Updated Apr 5, 2024Apr 5, 2024

• VorteX_m

  Public
  Java

  •00 forks•00 stars•00 issues•22 pull requests•Updated Jul 16, 2023Jul 16, 2023

• vortex

  Public
  VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:

  Java

  •66 forks•3434 stars•2121 issues•22 pull requests•Updated Apr 17, 2023Apr 17, 2023

• TissueSchematics

  Public
  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"

  Jupyter Notebook

  •22 forks•1212 stars•00 issues•00 pull requests•Updated Mar 3, 2023Mar 3, 2023

• RAPID

  Public
  RAPID: a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data

  MATLAB

  •

  GNU General Public License v3.0

  •22 forks•1212 stars•11 issue•00 pull requests•Updated Dec 3, 2022Dec 3, 2022

• Rclusterpp

  Public
  Memory efficient clustering in R for large datasets

  C++

  •

  Other

  •1111 forks•2222 stars•77 issues•22 pull requests•Updated Aug 22, 2022Aug 22, 2022

• CodexUpgrader

  Public
  This tool is to help Codex users upgrade their processed Codex data from Nolan lab tiff or old format to the new image sequence format that is compatible to be …

  Java

  •00 forks•00 stars•00 issues•22 pull requests•Updated May 20, 2022May 20, 2022

• CODEX

  Public
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation

  Java

  •

  MIT License

  •1212 forks•5353 stars•99 issues•33 pull requests•Updated May 20, 2022May 20, 2022

• SpatialScore

  Public
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphom…

  R

  •1111 forks•1717 stars•55 issues•00 pull requests•Updated Sep 26, 2021Sep 26, 2021

• sandbox

  Public
  Accessory algorithms and data structures for multivariate single-cell analysis. VorteX and CODEX projects use this library

  Java

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 13, 2021May 13, 2021

• CODEXMSICreator

  Public
  A visual studio project to create MSI for CODEX uploader and segmentation JAR

  00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2020Sep 22, 2020

• CodexNapariViewer

  Public
  A simple viewer for CODEX datasets developed using a python image analysis framework called napari.

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 4, 2020Sep 4, 2020

• CellVisionSegmenter

  Public
  Python

  •

  MIT License

  •2727 forks•33 stars•00 issues•00 pull requests•Updated Jun 23, 2020Jun 23, 2020

• cytofCore

  Public
  R package for working with CyToF data

  R

  •

  GNU General Public License v3.0

  •1515 forks•2727 stars•88 issues•00 pull requests•Updated May 11, 2020May 11, 2020

• codexstacktrimmer

  Public
  Trims the codex stacks leaving a specified number of slices around the given plane

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 1, 2019Jun 1, 2019

• diseffusion

  Public
  Comprehensive comparison of dimensionality reduction data for single-cell data

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 18, 2018Oct 18, 2018

• scaffold

  Public
  scaffold

  R

  •88 forks•1818 stars•1010 issues•00 pull requests•Updated Aug 13, 2018Aug 13, 2018

• CODEXServerSparkBuild

  Public
  Project to deploy the CODEX server on the left and right computers in the nolan lab.

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2018Jul 9, 2018

• single-cell-debarcoder

  Public
  deconvolution of barcoded CyTOF data

  MATLAB

  •

  GNU General Public License v3.0

  •2222 forks•88 stars•00 issues•00 pull requests•Updated May 26, 2018May 26, 2018

• bead-normalization

  Public
  bead-based normalization of mass cytometry data

  MATLAB

  •

  GNU General Public License v3.0

  •88 forks•1313 stars•1212 issues•00 pull requests•Updated May 26, 2018May 26, 2018

• CODEXServer

  Public
  Run CODEX apps on the web: driftcompensation, deconvolution, segmentation, clustering and viewing

  Java

  •

  GNU Lesser General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 23, 2018May 23, 2018

• SNAIL

  Public
  SNAIL paper data

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2018Apr 27, 2018

• CODEXViewer

  Public
  An ImageJ plugin to view and analyze CODEX images from the CODEXToolkit.

  Java

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 13, 2018Mar 13, 2018

• ScaleInvDBV

  Public
  Scale-invariant debarcoding algorithm for CyTOF data

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 9, 2018Jan 9, 2018

• scone

  Public
  The SCONE algorithm

  00 forks•00 stars•00 issues•00 pull requests•Updated May 16, 2017May 16, 2017

• PLAYRDesign

  Public
  A tool to design probes for the PLAYR technology

  JavaScript

  •11 fork•33 stars•77 issues•00 pull requests•Updated May 3, 2017May 3, 2017