Package: IDSL.CSA 1.2

Dinesh Barupal

IDSL.CSA: Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses

A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.

Authors:Sadjad Fakouri-Baygi [aut], Dinesh Barupal [cre, aut]

IDSL.CSA_1.2.tar.gz
IDSL.CSA_1.2.zip(r-4.5)IDSL.CSA_1.2.zip(r-4.4)IDSL.CSA_1.2.zip(r-4.3)
IDSL.CSA_1.2.tgz(r-4.4-any)IDSL.CSA_1.2.tgz(r-4.3-any)
IDSL.CSA_1.2.tar.gz(r-4.5-noble)IDSL.CSA_1.2.tar.gz(r-4.4-noble)
IDSL.CSA_1.2.tgz(r-4.4-emscripten)IDSL.CSA_1.2.tgz(r-4.3-emscripten)
IDSL.CSA.pdf |IDSL.CSA.html✨
IDSL.CSA/json (API)

# Install 'IDSL.CSA' in R:
install.packages('IDSL.CSA', repos = c('https://idslme.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/idslme/idsl.csa/issues

Datasets:

On CRAN:

composite-spectra-analysiscsadata-dependent-acquisitiondata-independent-acquisitionddadiamass-spectrometrymetabolomicsmetabolomics-pipelinesmall-moleculespectral-entropy

22 exports 5 stars 1.18 score 25 dependencies 237 downloads

Last updated 1 years agofrom:fd57739db5. Checks:ERROR: 1 OK: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILAug 21 2024
R-4.5-winOKAug 21 2024
R-4.5-linuxOKAug 21 2024
R-4.4-winOKAug 21 2024
R-4.4-macOKAug 21 2024
R-4.3-winOKAug 21 2024
R-4.3-macOKAug 21 2024

Exports:aligned_fragmentation_spectra_annotatorCSA_adductAnnotatorCSA_alignedMetaSpectraCatalogerCSA_alignedPeaksTanimotoCoefficientCalculatorCSA_AlignedTable_xlsxAnalyzerCSA_fragmentationPeakDetectionCSA_reference_xlsxAnalyzerCSA_workflowCSA_xlsxAnalyzerDDA_fragmentationPeakDetectionDDA_rawSpectraDeconvolutionDDA_workflowDDA_xlsxAnalyzerDDA2mspDIA_MS1_fragmentationPeakDetectionDIA_MS2_fragmentationPeakDetectionDIA_workflowDIA_xlsxAnalyzerIDSL.CSA_MSPgeneratorIDSL.CSA_referenceMSPgeneratorIDSL.CSA_workflowIDSL.CSA_xlsxAnalyzer

Dependencies:base64enccellrangerclicpp11crayonfansigluehmsIDSL.FSAIDSL.IPAIDSL.MXPlifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readxlrematchrlangtibbleutf8vctrsxml2

Readme and manuals

Help Manual

Help pageTopics
Aligned Fragmentation Spectra Annotatoraligned_fragmentation_spectra_annotator
CSA Adduct AnnotatorCSA_adductAnnotator
CSA Aligned Meta-Spectra CatalogerCSA_alignedMetaSpectraCataloger
CSA Aligned Peaks Tanimoto Coefficient CalculatorCSA_alignedPeaksTanimotoCoefficientCalculator
CSA Aligned Table xlsx AnalyzerCSA_AlignedTable_xlsxAnalyzer
CSA peakList MSP generationCSA_fragmentationPeakDetection
CSA PARAM SPECCSA_PARAM_SPEC
CSA reference xlsxAnalyzerCSA_reference_xlsxAnalyzer
CSA workflowCSA_workflow
CSA xlsx AnalyzerCSA_xlsxAnalyzer
DDA Fragmentation Peaks DetectionDDA_fragmentationPeakDetection
DDA Raw Spectra DeconvolutionDDA_rawSpectraDeconvolution
DDA WorkflowDDA_workflow
xlsx Analyzer for DDA analysisDDA_xlsxAnalyzer
DDA to mspDDA2msp
CSA DIA MS1 Fragmentation Peaks DetectionDIA_MS1_fragmentationPeakDetection
CSA DIA MS2 Fragmentation Peaks DetectionDIA_MS2_fragmentationPeakDetection
DIA WorkflowDIA_workflow
DIA xlsx Analyzer for DIA analysisDIA_xlsxAnalyzer
IDSL.CSA MSP GeneratorIDSL.CSA_MSPgenerator
IDSL.CSA Reference MSP GeneratorIDSL.CSA_referenceMSPgenerator
IDSL.CSA workflowIDSL.CSA_workflow
IDSL.CSA workflow xlsx AnalyzerIDSL.CSA_xlsxAnalyzer
negative adductsnegativeAdducts
positive adductspositiveAdducts