Visualization and cellular hierarchy inference of single-cell data using SPADE

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

Hierarchical clustering in minimum spanning trees

(2015) Meichen Yu et al.   CHAOS

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, Part 2: Biological evaluation

(2014) Tim R. Mosmann et al.   CYTOMETRY PART A

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells

(2014) Benedict Anchang et al.   PLoS Computational Biology

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Critical assessment of automated flow cytometry data analysis techniques

(2013) Nima Aghaeepour et al.   NATURE METHODS

Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)

(2013) K. Shekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data

(2012) M. D. Linderman et al.   BIOINFORMATICS

TreeVis: A MATLAB-based tool for tree visualization

(2012) Peng Qiu et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

RchyOptimyx: Cellular hierarchy optimization for flow cytometry

(2012) Nima Aghaeepour et al.   CYTOMETRY PART A

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Inferring Phenotypic Properties from Single-Cell Characteristics

(2012) Peng Qiu   PLoS One

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Discovering Biological Progression Underlying Microarray Samples

(2011) Peng Qiu et al.   PLoS Computational Biology

Data reduction for spectral clustering to analyze high throughput flow cytometry data

(2010) Habil Zare et al.   BMC BIOINFORMATICS

flowClust: a Bioconductor package for automated gating of flow cytometry data

(2009) Kenneth Lo et al.   BMC BIOINFORMATICS

Automated high-dimensional flow cytometric data analysis

(2009) S. Pyne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA