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>. The suggested packages 'entab' and 'chromConverterExtraTests' are not on CRAN: both are available from the repository given in 'Additional_repositories', and the latest test fixtures can also be installed from <https://github.com/ethanbass/chromConverterExtraTests>.
Last updated
cheminformaticschromatographyfair-datagc-fidhplchplc-dadhplc-uvmetabolomicsmetabolomics-dataopen-dataopen-science
7.97 score 58 stars 2 dependents 19 scripts 718 downloads
chromatographR - Chromatographic Data Analysis Toolkit
Analyzes chromatographic data from high performance liquid chromatography with diode-array or ultraviolet detection (HPLC-DAD/UV), as well as other detectors, in a high-throughput and reproducible workflow. Provides functionality for preprocessing, alignment, peak detection, peak model fitting, peak table construction, and data visualization. Chromatogram alignment is available via parametric time warping (as implemented in 'ptw') or variable penalty dynamic time warping (as implemented in 'VPdtw'). Peak detection is based on a first-derivative zero-crossing algorithm, and peak shapes are fitted using non-linear least squares. Underlying methodologies are described in: Wehrens et al. (2015) <doi:10.1007/s11306-014-0683-5> for preprocessing and peak table construction; Eilers (2004) <doi:10.1021/ac034800e> and Wehrens et al. (2015) <doi:10.1093/bioinformatics/btv299> for parametric time warping; Clifford & Stone (2012) <doi:10.18637/jss.v047.i08> for variable penalty dynamic time warping; Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm> for peak detection; Lan & Jorgenson (2001) <doi:10.1016/S0021-9673(01)00594-5> for exponential-Gaussian hybrid fitting; and Naish & Hartwell (1988) <doi:10.1007/BF02268168> for bi-exponentially modified Gaussian fitting.
Last updated
bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research
6.75 score 25 stars 1 dependents 15 scripts 41 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
clddata-visualizationggplot-extensionggplot2
3.95 score 3 stars 4 scriptsVPdtw - 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
chemoinformaticschemometricschromatographytime-seriestime-warpingcpp
3.78 score 2 stars 2 dependents 5 scripts 332 downloadsentab - Entab
Entab is a record-format file reader.
Last updated
rustcargo
2.78 score 1 stars 1 scriptsmzinspectr - 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
cheminformaticsgc-mslc-msmetabolomics
2.30 score 4 starsShinyChromViewer - Shiny Gadget for Interactive Viewing and Exploration of Chromatograms
Shiny Gadget for interactive viewing and exploration of chromatograms.
Last updated
chromatographyhplchplc-dadhplc-uvopen-dataopen-scienceshinyshiny-apps
2.18 score 3 starszerenebatchR - Utility for Batch Processing in Zerene Stacker
Writes Zerene Stacker batch files and executes them from the commandline.
Last updated
focus-stacking
2.00 score 2 starsr2zotero - Send Suggested R Package Citations Directly to Zotero
Facilitates the citation of R packages by importing citations from 'CITATION' file directly to a local Zotero library using the Zotero Web API.
Last updated
bibtexcitation-workflowscitationsreproducible-researchzotero
1.70 score