Pinned Repositories
citrus
Citrus Development Code
CODEX
Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
CODEXServer
Run CODEX apps on the web: driftcompensation, deconvolution, segmentation, clustering and viewing
CODEXServerSparkBuild
Project to deploy the CODEX server on the left and right computers in the nolan lab.
CODEXViewer
An ImageJ plugin to view and analyze CODEX images from the CODEXToolkit.
cytofCore
R package for working with CyToF data
NeighborhoodCoordination
Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"
scaffold
scaffold
spade
SPADE: Spanning Tree Progression of Density Normalized Events
vortex
VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
Garry P. Nolan Laboratory's Repositories
nolanlab/NeighborhoodCoordination
Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"
nolanlab/CODEX
Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
nolanlab/vortex
VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
nolanlab/citrus
Citrus Development Code
nolanlab/cytofCore
R package for working with CyToF data
nolanlab/Rclusterpp
Memory efficient clustering in R for large datasets
nolanlab/scaffold
scaffold
nolanlab/REDSEA
nolanlab/SpatialScore
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".
nolanlab/bead-normalization
bead-based normalization of mass cytometry data
nolanlab/RAPID
RAPID: a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data
nolanlab/TissueSchematics
Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
nolanlab/single-cell-debarcoder
deconvolution of barcoded CyTOF data
nolanlab/CellVisionSegmenter
nolanlab/PLAYRDesign
A tool to design probes for the PLAYR technology
nolanlab/cytof-backer-upper
Script for backing up CyTOF data to Google cloud storage
nolanlab/CodexNapariViewer
A simple viewer for CODEX datasets developed using a python image analysis framework called napari.
nolanlab/CODEXViewer
An ImageJ plugin to view and analyze CODEX images from the CODEXToolkit.
nolanlab/diseffusion
Comprehensive comparison of dimensionality reduction data for single-cell data
nolanlab/CODEXMSICreator
A visual studio project to create MSI for CODEX uploader and segmentation JAR
nolanlab/CODEXServer
Run CODEX apps on the web: driftcompensation, deconvolution, segmentation, clustering and viewing
nolanlab/CODEXServerSparkBuild
Project to deploy the CODEX server on the left and right computers in the nolan lab.
nolanlab/codexstacktrimmer
Trims the codex stacks leaving a specified number of slices around the given plane
nolanlab/CodexUpgrader
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.
nolanlab/sandbox
Accessory algorithms and data structures for multivariate single-cell analysis. VorteX and CODEX projects use this library
nolanlab/ScaleInvDBV
Scale-invariant debarcoding algorithm for CyTOF data
nolanlab/scone
The SCONE algorithm
nolanlab/SNAIL
SNAIL paper data
nolanlab/SPACEc
nolanlab/VorteX_m