Example 1 | Part 0. Setup | Set input directories | Part 1: Importing spectra files: nmr_import_spectra() | Part 2: Plotting the spectra: nmr_plot_spectra() | Part 3: Assigning compound classes: nmr_assign_bins() | Part 4: Calculating relative abundance of compound classes: nmr_relabund() | (a) import the peaks | (b) assign compound classes/bins to each peak | (c) calculate relative abundance | Part 5: Visualizing the processed relative abundance data | Example 2 | Importing your own preferred bin sets
Package: nmrrr 1.0.0
nmrrr: Binning and Visualizing NMR Spectra in Environmental Samples
A reproducible workflow for binning and visualizing NMR (nuclear magnetic resonance) spectra from environmental samples. The 'nmrrr' package is intended for post-processing of NMR data, including importing, merging and, cleaning data from multiple files, visualizing NMR spectra, performing binning/integrations for compound classes, and relative abundance calculations. This package can be easily inserted into existing analysis workflows by users to help with analyzing and interpreting NMR data.
Authors:
nmrrr_1.0.0.tar.gz
nmrrr_1.0.0.zip(r-4.7-any)nmrrr_1.0.0.zip(r-4.6-any)nmrrr_1.0.0.zip(r-4.5-any)
nmrrr_1.0.0.tgz(r-4.6-any)nmrrr_1.0.0.tgz(r-4.5-any)
nmrrr_1.0.0.tar.gz(r-4.7-any)nmrrr_1.0.0.tar.gz(r-4.6-any)
nmrrr_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nmrrr/json (API)
| # Install 'nmrrr' in R: |
| install.packages('nmrrr', repos = c('https://kaizadp.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kaizadp/nmrrr/issues
Datasets:
- bins_CadeMenun2015 - NMR grouping bins from Cade-Menun (2015).
- bins_Clemente2012 - NMR grouping bins from Clemente et al. (2012).
- bins_Hertkorn2013 - NMR grouping bins from Hertkorn et al. (2013).
- bins_Lynch2019 - NMR grouping bins from Lynch et al. (2019).
- bins_Mitchell2018 - NMR grouping bins from Mitchell et al. (2018).
- bins_ss_Baldock2004 - NMR grouping bins from Baldock et al. (2004).
- bins_ss_Clemente2012 - NMR grouping bins from Clemente et al. (2012) - ss.
- bins_ss_Preston2009 - NMR grouping bins from Preston et al. (2009).
Last updated from:c21d8f0f76. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 171 | ||
| source / vignettes | OK | 246 | ||
| linux-release | OK | 167 | ||
| macos-release | OK | 204 | ||
| macos-oldrel | OK | 157 | ||
| windows-devel | OK | 124 | ||
| windows-release | OK | 112 | ||
| windows-oldrel | OK | 119 | ||
| wasm-release | OK | 111 |
Exports:nmr_assign_binsnmr_import_peaksnmr_import_spectranmr_plot_spectranmr_relabund
Dependencies:askpassbitbit64bootcellrangerclassclicliprcpp11crayoncurldata.tableDescToolsdplyre1071Exactexpmfarverforcatsfsgenericsggplot2gldgluegtablehavenhmshttrisobandjsonlitelabelinglatticelifecyclelmommagrittrMASSMatrixmimemvtnormopensslpillarpkgconfigprettyunitsprogressproxypurrrR6RColorBrewerRcppreadrreadxlrematchrlangrootSolverstudioapiS7scalesstringistringrsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| NMR grouping bins from Cade-Menun (2015). | bins_CadeMenun2015 |
| NMR grouping bins from Clemente et al. (2012). | bins_Clemente2012 |
| NMR grouping bins from Hertkorn et al. (2013). | bins_Hertkorn2013 |
| NMR grouping bins from Lynch et al. (2019). | bins_Lynch2019 |
| NMR grouping bins from Mitchell et al. (2018). | bins_Mitchell2018 |
| NMR grouping bins from Baldock et al. (2004). | bins_ss_Baldock2004 |
| NMR grouping bins from Clemente et al. (2012) - ss. | bins_ss_Clemente2012 |
| NMR grouping bins from Preston et al. (2009). | bins_ss_Preston2009 |
| Assign compound classes using the chosen binset | nmr_assign_bins |
| Import and process picked peaks data | nmr_import_peaks |
| Import and process NMR spectral data | nmr_import_spectra |
| Plot NMR spectra | nmr_plot_spectra |
| Compute relative abundance for each sample | nmr_relabund |