Repositories list

• SPACEc

  Public
  Jupyter Notebook

  •

  Other

  •5•1•0•0•Updated Jan 30, 2025Jan 30, 2025

• NeighborhoodCoordination

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

  Jupyter Notebook

  •17•54•2•0•Updated Nov 4, 2024Nov 4, 2024

• cytof-backer-upper

  Public
  Script for backing up CyTOF data to Google cloud storage

  Python

  •1•2•0•0•Updated Jul 19, 2024Jul 19, 2024

• citrus

  Public
  Citrus Development Code

  R

  •

  GNU General Public License v3.0

  •20•31•46•0•Updated Apr 14, 2024Apr 14, 2024

• REDSEA

  Public
  Jupyter Notebook

  •

  Other

  •10•17•0•0•Updated Apr 5, 2024Apr 5, 2024

• VorteX_m

  Public
  Java

  •0•0•0•2•Updated Jul 16, 2023Jul 16, 2023

• vortex

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

  Java

  •6•34•21•2•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

  •2•10•0•0•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

  •1•11•1•0•Updated Dec 3, 2022Dec 3, 2022

• Rclusterpp

  Public
  Memory efficient clustering in R for large datasets

  C++

  •

  Other

  •11•20•7•2•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 used with MAV for analysis.

  Java

  •0•0•0•2•Updated May 20, 2022May 20, 2022

• CODEX

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

  Java

  •

  MIT License

  •11•45•8•3•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 lymphoma".

  R

  •8•14•2•0•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

  •0•0•0•0•Updated May 13, 2021May 13, 2021

• CODEXMSICreator

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

  0•0•0•0•Updated Sep 22, 2020Sep 22, 2020

• CodexNapariViewer

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

  Python

  •0•1•0•0•Updated Sep 4, 2020Sep 4, 2020

• CellVisionSegmenter

  Public
  Python

  •

  MIT License

  •25•3•0•0•Updated Jun 23, 2020Jun 23, 2020

• cytofCore

  Public
  R package for working with CyToF data

  R

  •

  GNU General Public License v3.0

  •15•26•8•0•Updated May 11, 2020May 11, 2020

• codexstacktrimmer

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

  Java

  •0•0•0•0•Updated Jun 1, 2019Jun 1, 2019

• diseffusion

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

  R

  •0•1•0•0•Updated Oct 18, 2018Oct 18, 2018

• scaffold

  Public
  scaffold

  R

  •8•18•10•0•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

  •0•0•0•0•Updated Jul 9, 2018Jul 9, 2018

• single-cell-debarcoder

  Public
  deconvolution of barcoded CyTOF data

  MATLAB

  •

  GNU General Public License v3.0

  •22•7•0•0•Updated May 26, 2018May 26, 2018

• bead-normalization

  Public
  bead-based normalization of mass cytometry data

  MATLAB

  •

  GNU General Public License v3.0

  •8•13•11•0•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

  •0•0•0•0•Updated May 23, 2018May 23, 2018

• SNAIL

  Public
  SNAIL paper data

  0•0•0•0•Updated Apr 27, 2018Apr 27, 2018

• CODEXViewer

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

  Java

  •0•1•0•0•Updated Mar 13, 2018Mar 13, 2018

• ScaleInvDBV

  Public
  Scale-invariant debarcoding algorithm for CyTOF data

  Java

  •0•0•0•0•Updated Jan 9, 2018Jan 9, 2018

• scone

  Public
  The SCONE algorithm

  0•0•0•0•Updated May 16, 2017May 16, 2017

• PLAYRDesign

  Public
  A tool to design probes for the PLAYR technology

  JavaScript

  •1•3•7•0•Updated May 3, 2017May 3, 2017