Package: gcxgclab 1.1.0

Stephanie Gamble

gcxgclab: GCxGC Preprocessing and Analysis

Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.

Authors:Stephanie Gamble [aut, cre], Mannion Joseph [ctb], Granger Caroline [ctb], Battelle Savannah River Alliance [cph], NNSA, US DOE [fnd]

gcxgclab_1.1.0.tar.gz
gcxgclab_1.1.0.tar.gz(r-4.7-any)gcxgclab_1.1.0.tar.gz(r-4.6-any)
gcxgclab_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gcxgclab/json (API)

# Install 'gcxgclab' in R:

install.packages('gcxgclab', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 2 scripts 225 downloads 34 exports 42 dependencies

Last updated from:f8cc7e62e5. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	143
source / vignettes	OK	182
linux-release-x86_64	OK	121
wasm-release	OK	116

Exports:align batch_eic batch_extract batch_ms batch_preprocess bl_corr comp_nist comp_peaks extract_data find_eic find_ms gauss gauss_fit gauss2 gauss2_fit mass_list nist_list non_targeted phase_shift plot_chr plot_defect plot_eic plot_gauss plot_gauss2 plot_ms plot_nist plot_peak plot_peakonly preprocess smooth targeted thr_peaks TIC_integrate top_peaks

Dependencies:cli cpp11 dplyr farver generics ggplot2 glue gtable isoband labeling lattice lhs lifecycle magrittr minpack.lm ncdf4 nilde nls.multstart pillar pkgconfig ptw purrr R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppDE Rdpack rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr zoo

gcxgclab: GCxGC Preprocessing and Analysis

Installation | Citation | Example | 1. Preprocessing | 2. Analysis

Rendered fromgcxgclab_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-11-25
Started: 2024-01-23

Help page	Topics
Reference Batch Align	align
Finds batch of EICs	batch_eic
Extracts data from all cdf files in a folder.	batch_extract
Finds batch of mass spectra	batch_ms
Batch reprocessing	batch_preprocess
Baseline correction	bl_corr
Compares MS to NIST MS database	comp_nist
Compare Peaks	comp_peaks
Extracts data from cdf file.	extract_data
Finds EICs	find_eic
Finds MS	find_ms
1D Gaussian function	gauss
Fitting to Gaussian curve	gauss_fit
2D Gaussian function	gauss2
Fitting to 2D Gaussian curve	gauss2_fit
Creates list of atomic mass data	mass_list
Creates list of NIST data	nist_list
Compares MS to atomic mass data	non_targeted
Phase shift	phase_shift
Plot chromatogram	plot_chr
Plots the Kendrick Mass Defect of a peak	plot_defect
Plots the EICs	plot_eic
Plots a peak with the fitted Gaussian curve.	plot_gauss
Plots a 3D peak with the fitted Gaussian curve.	plot_gauss2
Plots the mass spectra of a peak.	plot_ms
Plots the mass spectra of a NIST compound.	plot_nist
Peak Plot	plot_peak
Plot only peaks	plot_peakonly
Preprocessing	preprocess
Smoothing	smooth
Targeted Analysis	targeted
Threshold Peaks	thr_peaks
TIC integration	TIC_integrate
Top Peaks	top_peaks

Package: gcxgclab 1.1.0

gcxgclab: GCxGC Preprocessing and Analysis

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)