Introduction | bakedpi | Citing yamss | Dependencies | Processing a metabolomics dataset | Differential Analysis | Information contained in a CMSproc object | Density estimate | Sessioninfo | References
Package: yamss 1.39.0
Leslie Myint
yamss: Tools for high-throughput metabolomics
Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis. At the core of these methods is a peak detection phase that pools information across all samples simultaneously. This is in contrast to other methods that detect peaks in a sample-by-sample basis.
Authors:
yamss_1.39.0.tar.gz
yamss_1.39.0.zip(r-4.7)yamss_1.39.0.zip(r-4.6)yamss_1.39.0.zip(r-4.5)
yamss_1.39.0.tgz(r-4.6-any)yamss_1.39.0.tgz(r-4.5-any)
yamss_1.39.0.tar.gz(r-4.7-any)yamss_1.39.0.tar.gz(r-4.6-any)
yamss_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
yamss/json (API)
| # Install 'yamss' in R: |
| install.packages('yamss', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hansenlab/yamss/issues
Datasets:
- cmsRawExample - An example cmsRaw object
On BioConductor:yamss-1.39.0(bioc 3.24)yamss-1.38.0(bioc 3.23)
massspectrometrymetabolomicspeakdetectionsoftware
Last updated from:6ffd797767. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 217 | ||
| linux-devel-x86_64 | NOTE | 284 | ||
| source / vignettes | OK | 321 | ||
| linux-release-x86_64 | NOTE | 359 | ||
| macos-release-arm64 | NOTE | 264 | ||
| macos-oldrel-arm64 | NOTE | 259 | ||
| windows-devel | NOTE | 258 | ||
| windows-release | NOTE | 228 | ||
| windows-oldrel | NOTE | 266 | ||
| wasm-release | OK | 167 |
Exports:bakedpiCMSslicecolDatadensityCutoffdensityEstimatedensityQuantilesdiffrepgetEICSgetTICpeakBoundspeakQuantsplotDensityRegionreadMSdatashowslicepi
Dependencies:abindbase64encBiobaseBiocGenericsbiocmakebitopsbslibcachemclidata.tableDelayedArraydigestdir.expiryEBImageevaluatefastmapfftwtoolsfilelockfontawesomefsgenericsGenomicRangeshighrhtmltoolshtmlwidgetsIRangesjpegjquerylibjsonliteknitrlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemimemzRncdf4pngProtGenericsR6rappdirsRcppRCurlRhdf5librlangrmarkdownS4ArraysS4VectorssassSeqinfoSparseArraystatmodSummarizedExperimenttifftinytexxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Process raw data to compute density estimate. | bakedpi |
| A class to hold chromatography-mass spectrometry preprocessing information. | CMSproc-class densityEstimate densityQuantiles show,CMSproc-method |
| A class to hold chromatography-mass spectrometry raw data and metadata. | CMSraw-class colData,CMSraw-method show,CMSraw-method |
| An example cmsRaw object | cmsRawExample |
| A class to hold chromatography-mass spectrometry peak bounds and quantifications. | CMSslice CMSslice-class densityCutoff peakBounds peakQuants show,CMSslice-method |
| Perform differential analysis. | diffrep |
| Compute extracted ion chromatograms for multiple regions. | getEICS |
| Compute total ion chromatogram (TIC) for a sample. | getTIC |
| Image plot of region of density estimate. | plotDensityRegion |
| Read raw mass spectral data files. | readMSdata |
| Process raw data to compute density estimate. | slicepi |
