Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary
Repository
Rnmr1D is the main module in the NMRProcFlow web application
Basic Info
- Host: GitHub
- Owner: INRA
- Language: R
- Default Branch: master
- Homepage: http://nmrprocflow.org/
- Size: 19.8 MB
Statistics
- Stars: 8
- Watchers: 4
- Forks: 1
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
Rnmr1D
Rnmr1D is the main module in the NMRProcFlow web application (http://nmrprocflow.org) concerning the NMR spectra processing.
Inside NMRProcFlow, Rnmr1D allows users to process their NMR spectra within a GUI application and thus the macro-command sequence coming from this process can be saved.
Outside NMRProcFlow Rnmr1D become an R package allowing users to replay the macro-command sequence generated within NMRProcFlow. Moreover, without using NMRProcFlow, this package can also be used to replace any 'home-made script' by a macro-command sequence.
See the Macro-command Reference Guide to have more details about macro-commands.
Installation of some dependencies
You may need to install a C++ compiler if not the case yet (see https://teuder.github.io/rcpp4everyoneen/020install.html)
Some R packages from Bioconductor:
```R if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("impute","MassSpecWavelet","pcaMethods")) ```
Installation of the R package
- Note for Windows 11: Before performing the installation within R GUI it may require to specify the Compiler binaries path in the PATH environment variable so that the C++ code compilation will be correctly done ( check with Sys.getenv("PATH") ). Otherwise, install Rtools for Windows
R
if (!require("devtools"))
install.packages("devtools", repos="https://cran.rstudio.com")
devtools::install_github("INRA/Rnmr1D", dependencies = TRUE)
Example of use
```R library(Rnmr1D)
Test with the provided example data
datadir <- system.file("extra", package = "Rnmr1D") RAWDIR <- file.path(datadir, "CDBBI16P02") CMDFILE <- file.path(datadir, "NPmacrocmd.txt") SAMPLEFILE <- file.path(datadir, "Samples.txt")
Detect the number of Cores
detectCores()
Launch the pre-processing then the processing defined in the macro-command file
out <- Rnmr1D::doProcessing(RAWDIR, cmdfile=CMDFILE, samplefile=SAMPLEFILE, ncpu=detectCores())
Have a look on returned data structure
ls(out) ls(out$specMat)
Stacked Plot with a perspective effect
dev.new() plotSpecMat(out$specMat, ppm_lim=c(0.5,5), K=0.33)
Overlaid Plot
dev.new() plotSpecMat(out$specMat, ppm_lim=c(0.5,5), K=0, pY=0.1)
Get the data matrix
outMat <- getBucketsDataset(out, norm_meth='CSN')
Get the Signal/Noise Ratio (SNR) matrix
outSNR <- getSnrDataset(out, c(10.2,10.5), ratio=TRUE)
Get the bucket table
outBucket <- getBucketsTable(out)
Get the spectra data
spectra <- getSpectraData(out) ```
See a more complete illustation within the vignette
R
vignette("Rnmr1D")
You can access the vignette online : https://nmrprocflow.org/themes/html/Rnmr1D.html
Owner
- Name: Institut national de la recherche agronomique
- Login: INRA
- Kind: organization
- Location: France
- Website: http://www.inrae.fr/
- Repositories: 3
- Profile: https://github.com/INRA
Merged on 01/01/2020 with Irstea to become INRAE. See the new GitHub's organization called "INRAE".
GitHub Events
Total
- Push event: 20
Last Year
- Push event: 20
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| djacob65@gmail.com | d****5@g****m | 163 |
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 3
- Total pull requests: 0
- Average time to close issues: 2 days
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 3.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mkhpfister (2)
- vitor-mendes-iq (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 324 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
cran.r-project.org: Rnmr1D
Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
- Homepage: https://github.com/INRA/Rnmr1D
- Documentation: http://cran.r-project.org/web/packages/Rnmr1D/Rnmr1D.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
-
Latest release: 1.3.2
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.1.0 depends
- MASS >= 7.3 imports
- MassSpecWavelet >= 1.46.0 imports
- Matrix * imports
- Rcpp >= 0.12.7 imports
- XML >= 3.98 imports
- base64enc >= 0.1 imports
- doParallel >= 1.0.11 imports
- foreach >= 1.4.4 imports
- ggplot2 >= 3.0.0 imports
- igraph >= 1.2.1 imports
- impute >= 1.54.0 imports
- methods * imports
- minqa >= 1.2.4 imports
- plotly >= 4.8.0 imports
- plyr >= 1.8.4 imports
- ptw >= 1.9 imports
- signal >= 0.7 imports
- speaq >= 2.3.3 imports
- knitr * suggests
- rmarkdown * suggests