Package: yamss 1.33.0
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_1.33.0.tar.gz
yamss_1.33.0.zip(r-4.5)yamss_1.33.0.zip(r-4.4)yamss_1.33.0.zip(r-4.3)
yamss_1.33.0.tgz(r-4.4-any)yamss_1.33.0.tgz(r-4.3-any)
yamss_1.33.0.tar.gz(r-4.5-noble)yamss_1.33.0.tar.gz(r-4.4-noble)
yamss_1.33.0.tgz(r-4.4-emscripten)yamss_1.33.0.tgz(r-4.3-emscripten)
yamss.pdf |yamss.html✨
yamss/json (API)
NEWS
| # 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
- cmsRawExample - An example cmsRaw object
On BioConductor:yamss-1.33.0(bioc 3.21)yamss-1.32.0(bioc 3.20)
massspectrometrymetabolomicspeakdetectionsoftware
Last updated 23 days agofrom:2ec1eaf5fd. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 07 2024 |
| R-4.5-win | WARNING | Nov 07 2024 |
| R-4.5-linux | WARNING | Nov 07 2024 |
| R-4.4-win | WARNING | Nov 07 2024 |
| R-4.4-mac | NOTE | Nov 07 2024 |
| R-4.3-win | WARNING | Nov 07 2024 |
| R-4.3-mac | NOTE | Nov 07 2024 |
Exports:bakedpiCMSslicecolDatadensityCutoffdensityEstimatedensityQuantilesdiffrepgetEICSgetTICpeakBoundspeakQuantsplotDensityRegionreadMSdatashowslicepi
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbitopsbslibcachemclicrayoncurldata.tableDelayedArraydigestEBImageevaluatefastmapfftwtoolsfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshtmlwidgetshttrIRangesjpegjquerylibjsonliteknitrlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemimemzRncdf4opensslpngProtGenericsR6rappdirsRcppRCurlRhdf5librlangrmarkdownS4ArraysS4VectorssassSparseArraystatmodSummarizedExperimentsystifftinytexUCSC.utilsxfunXVectoryamlzlibbioc
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 |
