CODEX

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

User manual and downloads:

• https://github.com/nolanlab/CODEX
• https://github.com/nolanlab/CODEX/releases

Citrus

Description: Citrus is an algorithm that clusters cells from multiple samples (patients, stimulations, etc) into a hierarchical tree and then identifies the cell types from all levels of hierarchy that are significantly associated with the sample grouping, disease outcome, or response to specific stimulations.

Articles:

• Automated identification of stratifying signatures in cellular subpopulations.
• Robert V. Bruggner, Bernd Bodenmiller, David L. Dill, Robert J. Tibshirani, and Garry P. Nolan.
• PNAS 2014. http://www.pnas.org/content/111/26/E2770.abstract

User manual and downloads: https://github.com/nolanlab/citrus

SPADE

Description: SPADE is algorithm that organizes cells into minumum spanning trees of related phenotypes. MSTs facilitate the visualization of developmental lineages and comparison of functional markers across stimuli.

Articles:

• Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.
• Peng Qiu, Erin F Simonds, Sean C Bendall, Kenneth D Gibbs Jr, Robert V Bruggner, Michael D Linderman, Karen Sachs, Garry P Nolan & Sylvia K Plevritis.
• Nature biotechnology 2011 http://www.nature.com/nbt/journal/v29/n10/full/nbt.1991.html
•  

User manual and downloads:

• https://github.com/nolanlab/spade/wiki
• https://github.com/nolanlab/cytospade
• http://cytospade.org/

VorteX

Description:
VorteX Clustering Environment – Java graphical tool for single-cell analysis, clustering and visualization.

User downloads:
https://github.com/nolanlab/vortex
https://github.com/nolanlab/vortex/releases