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Protocols

OptimalCutpoints specifications

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Unique identifier OMICS_26843
Name OptimalCutpoints
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.1-3
Stability Stable
Maintained Yes

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  • person_outline Monica Lopez

Publication for OptimalCutpoints

OptimalCutpoints citations

 (35)
library_books

Metabolic alterations in urine extracellular vesicles are associated to prostate cancer pathogenesis and progression

2018
J Extracell Vesicles
PMCID: 5944373
PMID: 29760869
DOI: 10.1080/20013078.2018.1470442

[…] Change values and Bonferroni adjusted p-values.All statistical analyses were performed using R software v3.3.2 (R Development Core Team, 2016; http://cran.r-project.org) with stats, caret, psych and OptimalCutpoints package []. Boxplots and volcano plots were generated with ggplot2 R package. Correlations with clinical parameters such as BMI were done with cor.test function in R software, using S […]

library_books

Machine learning based diagnosis for disseminated intravascular coagulation (DIC): Development, external validation, and comparison to scoring systems

2018
PLoS One
PMCID: 5931474
PMID: 29718941
DOI: 10.1371/journal.pone.0195861

[…] luation was achieved via receiver operating characteristic (ROC) curve analysis, and calculation of AUC using the ‘pROC’ package []. The cut-off value (0.501) for the ANN model was determined by the ‘OptimalCutpoints’ package using the Youden method []. Statistical analyses were performed by Student’s t-test for parametric data and Mann-Whitney U test for non-parametric data. P values below 0.05 w […]

library_books

Stone heterogeneity index on single energy noncontrast computed tomography can be a positive predictor of urinary stone composition

2018
PLoS One
PMCID: 5896902
PMID: 29649219
DOI: 10.1371/journal.pone.0193945

[…] (ROC) curves using Youden methodology. Statistical analyses were performed using R software (version 3.3.2, R Foundation for Statistical Computing, Vienna, Austria; http://www.r-project.org) and its OptimalCutpoints package for determining the optimal cut-off values. […]

library_books

Diagnostic performance of intravoxel incoherent motion diffusion weighted imaging and dynamic contrast enhanced MRI for assessment of anal fistula activity

2018
PLoS One
PMCID: 5784995
PMID: 29370278
DOI: 10.1371/journal.pone.0191822

[…] Statistical analyses were performed by a bioinformatician (9 years of experience) using statistical software (R, version 3.2.5 including rjags, coda, pROC, OptimalCutpoints and MASS packages, R Foundation for Statistical Computing, Vienna, Austria). Categorical variables were expressed as numbers and percentages. Continuous variables were expressed as me […]

call_split

Diagnostic markers for the detection of ovarian cancer in BRCA1 mutation carriers

2017
PLoS One
PMCID: 5731824
PMID: 29244844
DOI: 10.1371/journal.pone.0189641
call_split See protocol

[…] Honest Significant Difference’ method. Multivariable discriminative models were built by logistic regressions and a cut-off defined by maximizing specificity and sensitivity simultaneously (R-package OptimalCutpoints). Receiver Operating Characteristic (ROC) curves, corresponding area under these ROC curves (AUC), and p-values are presented. (Two-sided) p-values below 0.05 were considered as stati […]

library_books

Urine cell free microRNA as biomarkers for transitional cell carcinoma

2017
BMC Res Notes
PMCID: 5708087
PMID: 29187235
DOI: 10.1186/s13104-017-2950-9

[…] discrimination ability, as conveyed by the receiver operating characteristics (ROC) curve, Fig. b. The sensitivity and specificity values of the miRNA-derived score, at three optimal cut-off points (“OptimalCutpoints” R package, using the minimization of misclassification criterion), are shown in Table . Fig. 2 […]


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OptimalCutpoints institution(s)
Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Universidade de Vigo, Vigo, Spain; Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
OptimalCutpoints funding source(s)
Supported by grants MTM2008-01603, MTM2010-09213-E and MTM2011- 28285-C02-00 from Spain’s Ministry of Science & Innovation and by Carlos III Institute of Health grant CA09/0053.

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