메뉴 건너뛰기




Volumn 12, Issue 9, 2016, Pages

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; CLUSTERING ALGORITHMS; CYTOLOGY; DATA VISUALIZATION; GRAPHICAL USER INTERFACES; INFORMATION ANALYSIS; PIPELINES; SET THEORY; T-CELLS; VISUALIZATION;

EID: 84989347290     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005112     Document Type: Article
Times cited : (265)

References (30)
  • 1
    • 68849103521 scopus 로고    scopus 로고
    • Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry
    • 19601617,..;: –.
    • Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, et al. Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem. 2009;81: 6813–6822. doi: 10.1021/ac901049w19601617
    • (2009) Anal Chem , vol.81 , pp. 6813-6822
    • Bandura, D.R.1    Baranov, V.I.2    Ornatsky, O.I.3    Antonov, A.4    Kinach, R.5    Lou, X.6
  • 7
    • 79955750055 scopus 로고    scopus 로고
    • Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
    • 21551058,..;: –.
    • Bendall SC, Simonds EF, Qiu P, Amir ED, Krutzik PO, Finck R, et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011;332: 687–696. doi: 10.1126/science.119870421551058
    • (2011) Science , vol.332 , pp. 687-696
    • Bendall, S.C.1    Simonds, E.F.2    Qiu, P.3    Amir, E.D.4    Krutzik, P.O.5    Finck, R.6
  • 8
    • 84919775675 scopus 로고    scopus 로고
    • Mass cytometry: a highly multiplexed single-cell technology for advancing drug development
    • 25349123,.;: –.
    • Atkuri KR, Stevens JC, Neubert H, Mass cytometry: a highly multiplexed single-cell technology for advancing drug development. Drug Metab Dispos. 2015;43: 227–33. doi: 10.1124/dmd.114.06079825349123
    • (2015) Drug Metab Dispos , vol.43 , pp. 227-233
    • Atkuri, K.R.1    Stevens, J.C.2    Neubert, H.3
  • 9
    • 84924258718 scopus 로고    scopus 로고
    • A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry
    • Zunder ER, Lujan E, Goltsev Y, Wernig M, Nolan GP, A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry. Cell Stem Cell. Elsevier Inc.; 2015;16: 323–337. doi: 10.1016/j.stem.2015.01.015
    • (2015) Cell Stem Cell. Elsevier Inc. , vol.16 , pp. 323-337
    • Zunder, E.R.1    Lujan, E.2    Goltsev, Y.3    Wernig, M.4    Nolan, G.P.5
  • 10
    • 84934442835 scopus 로고    scopus 로고
    • Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
    • Levine JH, Simonds EF, Bendall SC, Davis KL, Amir ED, Tadmor MD, et al. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell. Elsevier Inc.; 2015; 1–14. doi: 10.1016/j.cell.2015.05.047
    • (2015) Cell. Elsevier Inc. , pp. 1-14
    • Levine, J.H.1    Simonds, E.F.2    Bendall, S.C.3    Davis, K.L.4    Amir, E.D.5    Tadmor, M.D.6
  • 12
    • 84876799270 scopus 로고    scopus 로고
    • Normalization of mass cytometry data with bead standards
    • Finck R, Simonds E, Normalization of mass cytometry data with bead standards. Cytom Part …. 2013; 483–494. doi: 10.1002/cyto.a.22271
    • (2013) Cytom Part , pp. 483-494
    • Finck, R.1    Simonds, E.2
  • 13
    • 84856278095 scopus 로고    scopus 로고
    • Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8 + T Cell Phenotypes
    • Newell EW, Sigal N, Bendall SC, Nolan GP, Davis MM, Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8 + T Cell Phenotypes. Immunity. Elsevier Inc.; 2012;36: 142–152. doi: 10.1016/j.immuni.2012.01.002
    • (2012) Immunity. Elsevier Inc , vol.36 , pp. 142-152
    • Newell, E.W.1    Sigal, N.2    Bendall, S.C.3    Nolan, G.P.4    Davis, M.M.5
  • 15
    • 84891956083 scopus 로고    scopus 로고
    • Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)
    • 24344260,.;: –
    • Shekhar K, Brodin P, Davis MM, Chakraborty AK, Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE). Proc Natl Acad Sci U S A. 2013;111: 202–7. doi: 10.1073/pnas.1321405111/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.132140511124344260
    • (2013) Proc Natl Acad Sci U S A , vol.111 , pp. 202-207
    • Shekhar, K.1    Brodin, P.2    Davis, M.M.3    Chakraborty, A.K.4
  • 17
    • 84937638635 scopus 로고    scopus 로고
    • Mapping the Diversity of Follicular Helper T Cells in Human Blood and Tonsils Using High-Dimensional Mass Cytometry Analysis
    • Wong MT, Chen J, Narayanan S, Lin W, Anicete R, Kiaang HTK, et al. Mapping the Diversity of Follicular Helper T Cells in Human Blood and Tonsils Using High-Dimensional Mass Cytometry Analysis. Cell Rep. Elsevier; 2016;11: 1822–1833. doi: 10.1016/j.celrep.2015.05.022
    • (2016) Cell Rep. Elsevier , vol.11 , pp. 1822-1833
    • Wong, M.T.1    Chen, J.2    Narayanan, S.3    Lin, W.4    Anicete, R.5    Kiaang, H.T.K.6
  • 21
    • 84941753288 scopus 로고    scopus 로고
    • Diffusion maps for high-dimensional single-cell analysis of differentiation data
    • Haghverdi L, Buettner F, Theis FJ, Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics. 2015; 1–10. doi: 10.1093/bioinformatics/btv325
    • (2015) Bioinformatics , pp. 1-10
    • Haghverdi, L.1    Buettner, F.2    Theis, F.J.3
  • 22
    • 84977080410 scopus 로고    scopus 로고
    • Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development
    • Chen J, Schlitzer A, Chakarov S, Ginhoux F, Poidinger M, Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development. Nat Commun. Nature Publishing Group; 2016;7: 11988. doi: 10.1038/ncomms11988
    • (2016) Nat Commun. Nature Publishing Group , vol.7 , pp. 11988
    • Chen, J.1    Schlitzer, A.2    Chakarov, S.3    Ginhoux, F.4    Poidinger, M.5
  • 25
    • 84919775831 scopus 로고    scopus 로고
    • Accelerating t-SNE using Tree-Based Algorithms
    • Van Der Maaten L, Accelerating t-SNE using Tree-Based Algorithms. J Mach Learn Res. 2014;15(Oct): 3221–3245.
    • (2014) J Mach Learn Res , vol.15 , Issue.Oct , pp. 3221-3245
    • Van Der Maaten, L.1
  • 26
    • 84983315952 scopus 로고    scopus 로고
    • flowAI: automatic and interactive anomaly discerning tools for flow cytometry data
    • .; btw191–.
    • Monaco G, Chen H, Poidinger M, Chen J, de Magalhaes JP, Larbi A, flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. Bioinformatics. 2016; btw191–. doi: 10.1093/bioinformatics/btw191
    • (2016) Bioinformatics
    • Monaco, G.1    Chen, H.2    Poidinger, M.3    Chen, J.4    de Magalhaes, J.P.5    Larbi, A.6
  • 27
    • 84903289127 scopus 로고    scopus 로고
    • Clustering by fast search and find of density peaks
    • 24970081,.;: –.
    • Rodriguez A, Laio A, Clustering by fast search and find of density peaks. Science. 2014;344: 1492–6. doi: 10.1126/science.124207224970081
    • (2014) Science , vol.344 , pp. 1492-1496
    • Rodriguez, A.1    Laio, A.2
  • 28
    • 79961232797 scopus 로고    scopus 로고
    • The Split-Apply-Combine Strategy for Data
    • Wickham H, The Split-Apply-Combine Strategy for Data. J Stat Softw. 2011;40: 1–29.
    • (2011) J Stat Softw , vol.40 , pp. 1-29
    • Wickham, H.1
  • 29
    • 0020750980 scopus 로고
    • Percentage Points for a Generalized ESD Many-Outlier Procedure
    • Rosner B, Percentage Points for a Generalized ESD Many-Outlier Procedure. Technometrics. 1983;25: 165–172. doi: 10.2307/1268549
    • (1983) Technometrics , vol.25 , pp. 165-172
    • Rosner, B.1
  • 30


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.