quantro specifications

Information


Unique identifier OMICS_08842
Name quantro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
methods, RColorBrewer, BiocGenerics, Biobase, BiocStyle, ggplot2, RUnit, knitr, foreach, minfi, doParallel, iterators, R(>=3.1.3)
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Stephanie Hicks <>

Publication for quantro

quantro in publications

 (6)
PMCID: 5627434
PMID: 28974199
DOI: 10.1186/s12859-017-1847-x

[…] programming language: r., other requirements: dependencies: biobase. imports: biomart, downloader, edger, gplots, graphics, limma, matrixstats, preprocesscore, readr, rcolorbrewer, stats, quantro. suggests: knitr, rmarkdown, testthat (> = 0.8)., license: gplv3., any restrictions to use by non-academics: none., additional file 1: additional file 2: figure s1. additional file 3: […]

PMCID: 5526324
PMID: 28770015
DOI: 10.1186/s13148-017-0370-2

[…] probes with detection p values above 0.05, probes with less than three beads contributing to signal, and previously identified cross-reacting probes, for a total of 421,993 probes remaining []. quantro analysis indicated that quantile normalization was allowable, so we first normalized with the lumi quantile method, then with swan for probe type correction []. finally, we used combat […]

PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] where you do not expect global differences between your samples, for example a single tissue. further discussion on appropriate choice of normalisation can be found in ( ), and the accompanying quantro package includes data-driven tests for the assumptions of quantile normalisation. as we are comparing different blood cell types, which are globally relatively similar, we will apply […]

PMCID: 4736986
PMID: 26844019
DOI: 10.7717/peerj.1621

[…] (). the distribution of expression values for each condition in the simulated data is shown with violin plots (), which display an appreciable level of variability both within and between classes. quantro is a recently developed method for generating an f-score that represents the ratio of the within class variability to between class variability in the data () and is available as a package […]

PMCID: 4210944
PMID: 25348943
DOI: 10.1038/srep06797

[…] from the n2 adsorption and desorption isotherms at 77 k collected from an asap 2020 physisorption analyzer (micromeritics). x-ray photoelectron spectroscopy (xps) was carried out using a phi quantro sxm analyzer to analyze the chemical state of surface elements for the catalysts. the kinetic energies of photoelectrons were measured using a hemispherical electrostatic analyzer working […]


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quantro institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA

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