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MatchedFilter specifications

Information


Unique identifier OMICS_31121
Name MatchedFilter
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
First release date 2018
Stability Stable
Requirements
Numpy, scipy, scikit-learn, matplotlib, seaborn, metaseq, pybedtools
Maintained Yes

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Maintainer


  • person_outline Anurag Sethi <>

Publication for MatchedFilter

MatchedFilter in publications

 (8)
PMCID: 5220112
PMID: 28119698
DOI: 10.3389/fpls.2016.01954

[…] the application databridge from masslynx and processed using the xcms package as previously described (smith et al., ; zandalinas et al., ). chromatographic peak detection was performed using the matchedfilter algorithm, applying the following parameter settings: snr = 3, fwhm = 15 s, step = 0.01 d, mzdiff = 0.1 d, and profmethod = bin. retention time correction was achieved in three […]

PMCID: 4824825
PMID: 27110228
DOI: 10.1007/s11306-016-1023-8

[…] selection of analytically relevant features and data set annotation was developed, as shown in fig. .fig. 2, regarding peak detection, as preliminary works undertaken at our laboratory and using the matchedfilter algorithm were not successful, we selected the already implemented centwave algorithm, another peak detection algorithm (tautenhahn et al. ). this algorithm is based on the concomitant […]

PMCID: 4602305
PMID: 26459926
DOI: 10.1038/srep15126

[…] alignment of the data in the time domain and automatic integration and extraction of the peak intensities. xcms parameters were default settings (major default parameters: profmethod = bin; method = matchedfilter; step = 0.1) except for the following: full width at half maximum (fwhm) = 8, bandwidth (bw) = 10 and snthresh = 5, due to narrower peaks obtained by the use of the column packed […]

PMCID: 4423582
PMID: 25951936
DOI: 10.1186/1471-2105-16-S7-S1

[…] or more of these dimensions. for example, most proprietary ms software uses hard m/z bins for isotope trace extraction., the prominent algorithms for isotope trace extraction include centwave [], matchedfilter [], centroidpicker [], massifquant [], and maxquant []., matchedfilter operates on the simplifying assumptions that 1) isotope traces are completely contained within pre-processed hard […]

PMCID: 4329192
PMID: 25652567
DOI: 10.1186/s12870-015-0430-8

[…] masslynx v.4.1 and raw data files were analyzed using xcms following conversion to netcdf with the databridge software provided by masslynx. chromatographic peak detection was performed using the matchedfilter algorithm, applying the following parameter settings: snr = 3, fwhm = 15 s, step = 0.01 d, mzdiff = 0.1 da, and profmethod = bin. retention time correction was achieved in three […]


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MatchedFilter institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; School of Medicine, The Chinese University of Hong Kong, China; Department of Computer Science, The Chinese University of Hong Kong, China; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA; Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
MatchedFilter funding source(s)
Supported by the NIH grant HG009446-01, by NHLBI grant R24HL123879, and NHGRI grants R01HG003988, and U54HG006997, and UM1HG009421 and a Department of Energy Contract DE-AC02-05CH11231, University of California.

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