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ptw specifications

Information


Unique identifier OMICS_02392
Name ptw
Alternative name Parametric Time Warping
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 1.9-13
Stability Stable
Requirements
stats, graphics, grDevices, nloptr
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Tom Bloemberg

Publications for Parametric Time Warping

ptw citations

 (18)
library_books

PG Metrics: A chemometric based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability

2017
PLoS One
PMCID: 5645090
PMID: 29040278
DOI: 10.1371/journal.pone.0186197

[…] ment approaches are reported, e.g. correlation optimised warping (COW) [–], interval correlation shifting (icoshift) [–], msalign a MATLAB-bioinformatics tool [], dynamic time warping (DTW) [, –] and parametric time warping (PTW) [–]. Each one of these methods have different (i) algorithms to operate on, (ii) computational complexities to deal with, (iii) approaches to select the reference peaks, […]

library_books

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] ssing that exclusively perform peak detection or alignment, such as peak-grouping alignment [], an approach where information from grouping peaks within samples improves alignment across samples, and parametric time warping [], a fast alignment algorithm based on a variation of parametric time warping working on detected features rather than on complete profile data. In addition, combining single […]

library_books

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR based metabolomics

2017
Metabolomics
PMCID: 5313591
PMID: 28261014
DOI: 10.1007/s11306-017-1178-y

[…] n the ppm region. Indeed, for each spectra processing stage, at least two methods can be applied (see Supplementary Information S1). For instance, to align a spectral region with intertwined peaks, a Parametric Time Warping method (Bloemberg et al. ) will produce a better result provided that all spectra have the same amount of peaks within this region. Otherwise, a Least-Square algorithm will be […]

library_books

Fractionated stereotactic radiotherapy of benign skull base tumors: a dosimetric comparison of volumetric modulated arc therapy with Rapidarc® versus non coplanar dynamic arcs

2016
PMCID: 4835934
PMID: 27090091
DOI: 10.1186/s13014-016-0632-8

[…] when >95 % of the local gamma index values were above the criterion of 3 % and 3 mm []. For DA, the plans were verified using a punctual ionization chamber measurement (PinPoint® ionization chamber, PTW, Freiburg, Germany) positioned in a Lucy® 3D QA Phantom (Standard Imaging, Middleton, USA) and were accepted when the gap between the calculated and measured radiation dose was <2 %. […]

library_books

Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity

2016
Anal Bioanal Chem
PMCID: 4723632
PMID: 26753974
DOI: 10.1007/s00216-015-9241-x

[…] ešič [] and Draper et al. [] describe the possible steps in the data (pre)processing (processing pipeline). In this work, we have followed a slightly different order. Firstly, data were aligned using PTW, followed by a peak detection procedure, as described in the ‘’ section. The result of the application of such a processing pipeline is a reduced data set containing only peaks (including peak are […]

library_books

Pion effects in flattening filter‐free radiation beams

2015
PMCID: 5691018
PMID: 26699592
DOI: 10.1120/jacmp.v16i6.5869

[…] Manual Water Phantom (CNMC Company, Nashville TN), Wellhöfer IC10 (Scanditronix Wellhöfer North America, Bartlett, TN), and Exradin A19 ion (Standard Imaging, Middleton, WI) chambers together with a PTW UNIDOSE E electrometer (PTW‐Freiburg, Freiburg, Germany). Pion depends on the dose per pulse. We cannot directly control the dose per pulse coming out of the linac, but we can change the dose rate […]

Citations

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ptw institution(s)
Biometris, Wageningen UR, Wageningen, Netherlands

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