pROC: an open-source package for R and S+ to analyze and compare ROC curves
Xavier Robin,Natacha Turck,Alexandre Hainard,Natalia Tiberti,Frédérique Lisacek,Jean-Charles Sanchez,Markus Müller +6 more
TLDR
pROC as mentioned in this paper is a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface.Abstract:
Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/
under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.read more
Citations
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Journal ArticleDOI
A faecal microbiota signature with high specificity for pancreatic cancer
Ece Kartal,Thomas Schmidt,Esther Molina-Montes,Sandra Rodriguez-Perales,Jakob Wirbel,Oleksandr M. Maistrenko,Wasiu Akanni,Bilal Alashkar Alhamwe,Renato J. Alves,Alfredo Carrato,Hans-Peter Erasmus,Lidia Estudillo,Fabian Finkelmeier,Anthony Fullam,Anna Głazek,Paulina Gomez-Rubio,Rajna Hercog,Ferris Jung,Stefanie Kandels,Stephan Kersting,Melanie Langheinrich,Mirari Marquez,Xavier Molero,Askarbek N Orakov,Thea Van Rossum,Raúl Torres-Ruiz,Anja Telzerow,Konrad Zych,Vladimir Benes,Georg Zeller,Jonel Trebicka,Francisco X. Real,Núria Malats,Peer Bork +33 more
TL;DR: Faecal metagenomic classifiers performed much better than saliva-based classifiers and identified patients with PDAC with an accuracy of up to 0.84 area under the receiver operating characteristic curve (AUROC) based on a set of 27 microbial species, with consistent accuracy across early and late disease stages.
Journal ArticleDOI
A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.
Dianna Ng,Andrea Granados,Yale A. Santos,Venice Servellita,Gregory M. Goldgof,Cem Meydan,Alicia Sotomayor-Gonzalez,Andrew G. Levine,Joanna Balcerek,Lucy M. Han,Naomi Akagi,Kent Truong,Neil M. Neumann,David N. Nguyen,Sagar P. Bapat,Jing Cheng,Claudia Sanchez San Martin,Scot Federman,Jonathan Foox,Allan Gopez,Tony Li,Ray Chan,Cynthia S. Chu,Chiara A. Wabl,Amelia S. Gliwa,Kevin Reyes,Chao-Yang Pan,Hugo Guevara,Debra A. Wadford,Steve Miller,Christopher E. Mason,Charles Y. Chiu +31 more
TL;DR: This paper used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with severe acute respiratory syndrome coronavirus disease-19 (COVID-19) and controls, showing a muted immune response relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical downregulation of several key differentially expressed genes.
Journal ArticleDOI
Discordant transmission of bacteria and viruses from mothers to babies at birth.
Rabia Maqsood,Rabia Maqsood,Rachel Rodgers,Cynthia Rodriguez,Scott A. Handley,I. Malick Ndao,Phillip I. Tarr,Barbara B. Warner,Efrem S. Lim,Efrem S. Lim,Lori R. Holtz +10 more
TL;DR: Differences of the inter-generation transmissibility at birth between the major kingdoms of microbes indicate that the foundation of these microbial communities are shaped by different rules.
Journal ArticleDOI
Circulating microRNA as a biomarker for recovery in pediatric dilated cardiomyopathy
Shelley D. Miyamoto,Anis Karimpour-Fard,Valencia Peterson,Scott R. Auerbach,Kurt R. Stenmark,Brian L. Stauffer,Carmen C. Sucharov +6 more
TL;DR: A unique biomarker signature of miRNAs that are specific to children with DCM who have the potential to recover would be valuable in risk stratification of this challenging patient population.
Journal ArticleDOI
Predicting mortality in bronchiectasis using bronchiectasis severity index and FACED scores: a 19-year cohort study.
TL;DR: This study provides further validation of the FACED and BSI scores for the prediction of mortality in bronchiectasis and demonstrates their utility over a longer period than originally described.
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