Open-Source Software for Single-Cell Data Analysis
Computational tools developed by the Nolan Lab, freely available for the research community.
CODEX
Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
Citrus
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
SPADE
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