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 (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (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.

Last updated 4 days ago

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

6.20 score 14 stars 1 packages 9 scripts 39 downloads

chromConverter - Chromatographic File Converter

Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw', and 'Varian Workstation' files as well as various text-based 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>.

Last updated 7 days ago

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

6.11 score 28 stars 2 packages 11 scripts 538 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>).

Last updated 3 months ago

chemoinformaticschemometricschromatographytime-seriestime-warping

4.43 score 2 stars 3 packages 2 scripts 401 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).

Last updated 2 years ago

clddata-visualizationggplot-extensionggplot2

3.00 score 2 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.

Last updated 30 days ago

cheminformaticsgc-mslc-msmetabolomics

2.78 score 2 stars

zerenebatchR - Utility for Batch Processing in Zerene Stacker

Writes Zerene Stacker batch files and executes them from the commandline.

Last updated 8 months ago

focus-stacking

2.00 score 1 stars

ShinyChromViewer - Shiny Gadget for Interactive Viewing and Exploration of Chromatograms

Shiny Gadget for interactive viewing and exploration of chromatograms.

Last updated 2 years ago

chromatographyhplchplc-dadhplc-uvopen-dataopen-scienceshinyshiny-apps

2.00 score 2 stars