Cromwell statistics

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Cromwell specifications


Unique identifier OMICS_04669
Name Cromwell
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for Cromwell

Cromwell in publications

PMCID: 3116487
PMID: 21554713
DOI: 10.1186/1471-2105-12-140

[…] implementing the complete work-flow is available. commonly used public domain software tools are r and bioconductor [] packages like msprocess or process [], matlab packages like limpic [] or cromwell [] and the comprehensive c++ library openms [,]., statistical tests such as anova require intensity data for each feature to be normally distributed and the variance to be independent […]

PMCID: 3085423
PMID: 21552492
DOI: 10.4137/CIN.S6438

[…] maximized the cross-correlation between corrected spectra, using matlab version 7.0.1 (the mathworks, natick ma)., we used the udwt with a threshold of 20 to denoise the mean spectrum, using the cromwell software package;, local maxima in the denoised mean spectrum were identified as peaks. intervals containing the peaks and the location of the maxima within intervals were recorded. peak […]

PMCID: 2935426
PMID: 20823336
DOI: 10.1093/bioinformatics/btq397

[…] cruz-marcelo et al. () and emanuele and gurbaxani () presented the extensive studies to compare the performance of state-of-the-art methods for seldi data preprocessing, including cwt (du et al., ), cromwell (coombes et al., ; morris et al., ), process (li et al., ), ciphergen and specalign (wong et al., ). they concluded that cwt (du et al., ) has the best performance. another method which also […]

PMCID: 2689848
PMID: 19442271
DOI: 10.1186/1477-5956-7-19

[…] as an example of high throughput mass-spectrometry data. we perform a systematic comparison of two commonly used pre-processing methods as implemented in ciphergen proteinchip software and in the cromwell package. with respect to reproducibility, ciphergen and cromwell pre-processing are largely comparable. we find that the overlap between peaks detected by either ciphergen proteinchip […]

PMCID: 2631518
PMID: 19126200
DOI: 10.1186/1471-2105-10-4

[…] the following:, here "s" denotes smoothing filter, "b" denotes baseline correction method, "p" denotes peak finding criterion and "-" means smoothing or baseline correction method is not used. cromwell, limpic, lms, cwt, and process are designed for single spectrum peak detection. lcms-2d, mapquant, msinspect, mzmine, openms and xcms are designed for lc-ms (liquid chromatography mass […]

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Cromwell institution(s)
Department of Biostatistics and Applied Mathematics, The University of Texas M D Anderson Cancer Center, Houston, TX, USA

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