title: Automated mapping of phenotype space with single-cell data.
abstract: Accurate identification of cell subsets in complex populations is key to discovering novelty in multidimensional single-cell experiments. We present X-shift (http://web.stanford.edu/~samusik/vortex/), an algorithm that processes data sets using fast k-nearest-neighbor estimation of cell event density and arranges populations by marker-based classification. X-shift enables automated cell-subset clustering and access to biological insights that 'prior knowledge' might prevent the researcher from discovering.
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Samusik
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.|Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Zinaida
authors.initials: Z
authors.lastname: Good
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.|Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Spitzer
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.|Department of Pediatric Hematology and Oncology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Kara L
authors.initials: KL
authors.lastname: Davis
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Garry P
authors.initials: GP
authors.lastname: Nolan
mesh_terms: D000465:Algorithms; D000818:Animals; D001854:Bone Marrow Cells / Q000166:cytology; D016000:Cluster Analysis; D007089:Image Enhancement; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008297:Male; D008810:Mice, Inbred C57BL; D010363:Pattern Recognition, Automated / Q000379:methods*; D012680:Sensitivity and Specificity; D059010:Single-Cell Analysis / Q000379:methods*