-
1
-
-
42049123647
-
Automated gating of flow cytometry data via robust model-based clustering
-
Lo K, Brinkman R, Gottardo R. Automated gating of flow cytometry data via robust model-based clustering. Cytom A 2008;73A:321-332.
-
(2008)
Cytom A
, vol.73A
, pp. 321-332
-
-
Lo, K.1
Brinkman, R.2
Gottardo, R.3
-
2
-
-
77957550165
-
Misty mountain clustering: Application to fast unsupervised flow cytometry gating
-
Sugar I, Sealfon S. Misty mountain clustering: Application to fast unsupervised flow cytometry gating. BMC Bioinform 2010;11:502.
-
(2010)
BMC Bioinform
, vol.11
, pp. 502
-
-
Sugar, I.1
Sealfon, S.2
-
3
-
-
77954938186
-
Data reduction for spectral clustering to analyze high throughput flow cytometry data
-
Zare H, Shooshtari P, Gupta A, Brinkman R. Data reduction for spectral clustering to analyze high throughput flow cytometry data. BMC Bioinform 2010;11:403.
-
(2010)
BMC Bioinform
, vol.11
, pp. 403
-
-
Zare, H.1
Shooshtari, P.2
Gupta, A.3
Brinkman, R.4
-
5
-
-
84880849822
-
Hierarchical modeling for rare event detection and cell subsgnment across flow cytometry samples
-
Cron A, Gouttefangeas C, Frelinger J, Lin L, Singh SK, Britten CM, Welters MJP, van der Burg SH, West M, Chan C. Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples. PLoS Computat Biol 2013;9:e1003130.
-
(2013)
PLoS Computat Biol
, vol.9
, pp. e1003130
-
-
Cron, A.1
Gouttefangeas, C.2
Frelinger, J.3
Lin, L.4
Singh, S.K.5
Britten, C.M.6
Welters, M.J.P.7
van der Burg, S.H.8
West, M.9
Chan, C.10
-
6
-
-
84865139571
-
flowPeak: A fast unsupervised clustering for flow cytometry data via K-means and density peak finding
-
Ge Y, Sealfon S. flowPeak: A fast unsupervised clustering for flow cytometry data via K-means and density peak finding. Bioinformatics 2014;28:2052-2058.
-
(2014)
Bioinformatics
, vol.28
, pp. 2052-2058
-
-
Ge, Y.1
Sealfon, S.2
-
7
-
-
84899064968
-
Swift: Scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, part 1: Algorithm design
-
Naim I, Datta S, Rebhahn J, Cavenaugh JS, Mosmann TR, Sharma G. Swift: Scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, part 1: Algorithm design. Cytom A 2014;85A:408-421.
-
(2014)
Cytom A
, vol.85A
, pp. 408-421
-
-
Naim, I.1
Datta, S.2
Rebhahn, J.3
Cavenaugh, J.S.4
Mosmann, T.R.5
Sharma, G.6
-
8
-
-
84903722445
-
Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data
-
Pyne S, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng S, Hafler D, Levy R, Nolan GP, et al. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. Plos One 2014;9:e100334.
-
(2014)
Plos One
, vol.9
, pp. e100334
-
-
Pyne, S.1
Wang, K.2
Irish, J.3
Tamayo, P.4
Nazaire, M.D.5
Duong, T.6
Ng, S.7
Hafler, D.8
Levy, R.9
Nolan, G.P.10
-
9
-
-
84874666550
-
Critical assessment of automated flow cytometry data analysis techniques
-
FlowCAP Consortium, DREAM Consortium
-
Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium, Hoos HH, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods 2013;10:228-238.
-
(2013)
Nat Methods
, vol.10
, pp. 228-238
-
-
Aghaeepour, N.1
Finak, G.2
Hoos, H.H.3
Mosmann, T.R.4
Brinkman, R.5
Gottardo, R.6
Scheuermann, R.H.7
-
10
-
-
84859246989
-
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays
-
Aghaeepour N, Chattopadhyay PK, Ganesan A, O'Neill K, Zare H, Jalali A, Hoos HH, Roederer M, Brinkman RR. Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. Bioinformatics 2012;28:1009-1016.
-
(2012)
Bioinformatics
, vol.28
, pp. 1009-1016
-
-
Aghaeepour, N.1
Chattopadhyay, P.K.2
Ganesan, A.3
O'Neill, K.4
Zare, H.5
Jalali, A.6
Hoos, H.H.7
Roederer, M.8
Brinkman, R.R.9
-
11
-
-
84899506044
-
Enhanced flowType/RchyOptimyx: A bioconductor pipeline for discovery in high-dimensional cytometry data
-
O'Neill K, Jalali A, Aghaeepour N, Hoos H, Brinkman RR. Enhanced flowType/RchyOptimyx: A bioconductor pipeline for discovery in high-dimensional cytometry data. Bioinformatics 2014;30:1329-1330.
-
(2014)
Bioinformatics
, vol.30
, pp. 1329-1330
-
-
O'Neill, K.1
Jalali, A.2
Aghaeepour, N.3
Hoos, H.4
Brinkman, R.R.5
-
12
-
-
84903703398
-
Automated identification of stratifying signatures in cellular subpopulations
-
Bruggner RV, Bodenmiller B, Dill DL, Tibshirani RJ, Nolan GP. Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci USA 2014;111:E2770-E2777.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. E2770-E2777
-
-
Bruggner, R.V.1
Bodenmiller, B.2
Dill, D.L.3
Tibshirani, R.J.4
Nolan, G.P.5
-
13
-
-
75649145950
-
Immunologic and virologic events in early HIV infection predict subsequent rate of progression
-
Ganesan A, Chattopadhyay PK, Brodie TM, Qin J, Gu W, Mascola JR, Michael NL, Follmann DA, Roederer M. Immunologic and virologic events in early HIV infection predict subsequent rate of progression. J Infect Dis 2010;201:272-284.
-
(2010)
J Infect Dis
, vol.201
, pp. 272-284
-
-
Ganesan, A.1
Chattopadhyay, P.K.2
Brodie, T.M.3
Qin, J.4
Gu, W.5
Mascola, J.R.6
Michael, N.L.7
Follmann, D.A.8
Roederer, M.9
-
14
-
-
33745697199
-
Cox Proportional-Hazards Regression for Survival Data in R
-
2nd ed. Thousand Oaks CA: Sage .
-
Fox J, Weisberg S. Cox Proportional-Hazards Regression for Survival Data in R An R Companion to Applied Regression, 2nd ed. Thousand Oaks CA: Sage 2011.
-
(2011)
An R Companion to Applied Regression
-
-
Fox, J.1
Weisberg, S.2
-
15
-
-
0023441165
-
Time, a quality-control parameter in flow cytometry
-
Watson JV. Time, a quality-control parameter in flow cytometry. Cytometry 1987;8:646-649.
-
(1987)
Cytometry
, vol.8
, pp. 646-649
-
-
Watson, J.V.1
-
16
-
-
84983137943
-
-
flowClean: flowClean. R package version 1.2.0.
-
Fletez-Brant K. flowClean: flowClean. R package version 1.2.0. http://www.bioconductor.org/packages/release/bioc/html/flowClean.html
-
-
-
Fletez-Brant, K.1
-
17
-
-
33646361583
-
GenePattern 2.0
-
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet 2006;38:500-501.
-
(2006)
Nat Genet
, vol.38
, pp. 500-501
-
-
Reich, M.1
Liefeld, T.2
Gould, J.3
Lerner, J.4
Tamayo, P.5
Mesirov, J.P.6
-
18
-
-
77956489942
-
OMIP-001: Quality and phenotype of Ag-responsive human T-cells
-
Mahnke YD, Roederer M. OMIP-001: Quality and phenotype of Ag-responsive human T-cells. Cytom A 2010;77A:819-820.
-
(2010)
Cytom A
, vol.77A
, pp. 819-820
-
-
Mahnke, Y.D.1
Roederer, M.2
-
19
-
-
84890588882
-
flowCore: Basic structures for flow cytometry data
-
R package version 1.32.0.
-
Ellis B, Haaland P, Hahne F, Le Meur N, Gopalakrishnan N, Spidlen J. flowCore: Basic structures for flow cytometry data. R package version 1.32.0. http://www.bioconductor.org/packages/release/bioc/html/flowCore.html
-
-
-
Ellis, B.1
Haaland, P.2
Hahne, F.3
Le Meur, N.4
Gopalakrishnan, N.5
Spidlen, J.6
-
20
-
-
84928189767
-
flowDensity: Reproducing manual gating of flow cytometry data by automated density-based cell population identification
-
Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR. flowDensity: Reproducing manual gating of flow cytometry data by automated density-based cell population identification. Bioinformatics 2015;31:606-607.
-
(2015)
Bioinformatics
, vol.31
, pp. 606-607
-
-
Malek, M.1
Taghiyar, M.J.2
Chong, L.3
Finak, G.4
Gottardo, R.5
Brinkman, R.R.6
-
23
-
-
0030069896
-
Tutorial in biostatistics multivariable prognostic models: Issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors
-
Harrell FE, Lee KL, Mark DB. Tutorial in biostatistics multivariable prognostic models: Issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. Stat Med 1996;15:361-387.
-
(1996)
Stat Med
, vol.15
, pp. 361-387
-
-
Harrell, F.E.1
Lee, K.L.2
Mark, D.B.3
-
24
-
-
84946220296
-
Random Forests for Survival, Regression and Classification (RF-SRC)
-
Ishwaran H, Kogalur UB. Random Forests for Survival, Regression and Classification (RF-SRC). R package version 1.5.5. 2014. https://cran.r-project.org/web/packages/randomForestSRC/
-
(2014)
R package version 1.5.5.
-
-
Ishwaran, H.1
Kogalur, U.B.2
-
25
-
-
84863302503
-
Coordinate descent methods for the penalized semiparametric additive hazards model
-
Gorst-Rasmussen A, Scheike TH. Coordinate descent methods for the penalized semiparametric additive hazards model. J Stat Software 2012;47:1-17.
-
(2012)
J Stat Software
, vol.47
, pp. 1-17
-
-
Gorst-Rasmussen, A.1
Scheike, T.H.2
-
26
-
-
77954223563
-
FlowFP: A bioconductor package for fingerprinting flow cytometric data
-
Rogers WT, Holyst HA. FlowFP: A bioconductor package for fingerprinting flow cytometric data. Adv Bioinform 2009. Article ID 193947, 11 pages.
-
(2009)
Adv Bioinform
, pp. 11
-
-
Rogers, W.T.1
Holyst, H.A.2
-
27
-
-
80054768631
-
Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE
-
Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol 2011;29:886-891.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 886-891
-
-
Qiu, P.1
Simonds, E.F.2
Bendall, S.C.3
Gibbs, K.D.4
Bruggner, R.V.5
Linderman, M.D.6
Sachs, K.7
Nolan, G.P.8
Plevritis, S.K.9
-
28
-
-
84932195404
-
gEM/GANN: A multivariate computational strategy for auto-characterizing relationships between cellular and clinical phenotypes and predicting disease progression time using high-dimensional flow cytometry data
-
Tong DL, Ball GR, Pockley AG. gEM/GANN: A multivariate computational strategy for auto-characterizing relationships between cellular and clinical phenotypes and predicting disease progression time using high-dimensional flow cytometry data. Cytom A 2015;87:616-623.
-
(2015)
Cytom A
, vol.87
, pp. 616-623
-
-
Tong, D.L.1
Ball, G.R.2
Pockley, A.G.3
-
29
-
-
77954296648
-
Good cell, bad cell: Flow cytometry reveals T-cell subsets important in HIV disease
-
Chattopadhyay PK, Roederer M. Good cell, bad cell: Flow cytometry reveals T-cell subsets important in HIV disease. Cytom A 2010;77A:614-622.
-
(2010)
Cytom A
, vol.77A
, pp. 614-622
-
-
Chattopadhyay, P.K.1
Roederer, M.2
|