R-universe - ethanbass (Ethan Bass)

chromConverter - Chromatographic File Converter

Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Agilent OpenLab', 'Shimadzu LabSolutions', 'ThermoRaw', 'Varian Workstation', and 'Waters Empower' files as well as various other formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.

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cheminformaticschromatographyfair-datagc-fidhplchplc-dadhplc-uvmetabolomicsmetabolomics-dataopen-dataopen-science

6.61 score 49 stars 2 dependents 12 scripts 479 downloads

chromatographR - Chromatographic Data Analysis Toolset

Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.

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bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research

6.40 score 24 stars 1 dependents 9 scripts 6 downloads

VPdtw - Variable Penalty Dynamic Time Warping

Variable Penalty Dynamic Time Warping (VPdtw) for aligning chromatographic signals. With an appropriate penalty this method performs good alignment of chromatographic data without deforming the peaks (Clifford, D., Stone, G., Montoliu, I., Rezzi S., Martin F., Guy P., Bruce S., and Kochhar S.(2009) <doi:10.1021/ac802041e>; Clifford, D. and Stone, G. (2012) <doi:10.18637/jss.v047.i08>).

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chemoinformaticschemometricschromatographytime-seriestime-warpingcpp

3.78 score 2 stars 2 dependents 5 scripts 246 downloads

ggtukey - Compact Letter Displays for Multiple Comparisons in 'ggplot2'

Provides a simple interface to visualize paired comparisons in 'ggplot2' by adding compact letter displays (i.e. Tukey letters).

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clddata-visualizationggplot-extensionggplot2

3.48 score 3 stars 4 scripts

mzinspectr - Read and Analyze Mass Spectrometry Alignment Files

A few functions for analyzing MS-DIAL alignments in R. Includes functions for feature normalization, subtraction of blanks, and mass library (msp) search.

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cheminformaticsgc-mslc-msmetabolomics

2.60 score 4 stars