Package: IDSL.FSA 1.2

Dinesh Barupal

IDSL.FSA: Fragmentation Spectra Analysis (FSA)

The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.

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

IDSL.FSA_1.2.tar.gz
IDSL.FSA_1.2.zip(r-4.5)IDSL.FSA_1.2.zip(r-4.4)IDSL.FSA_1.2.zip(r-4.3)
IDSL.FSA_1.2.tgz(r-4.4-any)IDSL.FSA_1.2.tgz(r-4.3-any)
IDSL.FSA_1.2.tar.gz(r-4.5-noble)IDSL.FSA_1.2.tar.gz(r-4.4-noble)
IDSL.FSA_1.2.tgz(r-4.4-emscripten)IDSL.FSA_1.2.tgz(r-4.3-emscripten)
IDSL.FSA.pdf |IDSL.FSA.html✨
IDSL.FSA/json (API)

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

Peer review:

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

Datasets:

On CRAN:

fragmentation-spectramass-spectrometrymassbankmgfmgf-parsermspmsp-parserspectral-entropy

40 exports 1 stars 1.40 score 0 dependencies 2 dependents 251 downloads

Last updated 1 months agofrom:382f86d953. Checks:ERROR: 1 OK: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 18 2024
R-4.5-winOKSep 18 2024
R-4.5-linuxOKSep 18 2024
R-4.4-winOKSep 18 2024
R-4.4-macOKSep 18 2024
R-4.3-winOKSep 18 2024
R-4.3-macOKSep 18 2024

Exports:fragmentation_spectra_annotatorFSA_aggregateFSA_annotation_text_repelFSA_dir.createFSA_FSdb_xlsxAnalyzerFSA_loadRdataFSA_locate_regexFSA_logRecorderFSA_messageFSA_msp_annotatorFSA_msp2CytoscapeFSA_plotFSdb2SpectraFSA_R.aggregateFSA_spectra_marker_generatorFSA_SpectraSimilarity_xlsxAnalyzerFSA_uniqueMSPblockTaggerFSA_uniqueMSPblockTaggerUntargetedFSA_workflowFSA_xlsxAnalyzerFSdb_file_generatorFSdb_subsetterFSdb2mspFSdb2PeakXcolSubsetterFSdb2precursorTypemgf2mspmsp2FSdbmsp2TrainingMatrixmspPosNegSplitterplotFSdb2SpectraCorespectra_1A1B_mixerspectra_integratorspectra_ion_filterspectral_entropy_calculatorspectral_entropy_similarity_scoreUFSA_element_sorterUFSA_formula_vector_generatorUFSA_hill_molecular_formula_printerUFSA_ionization_pathway_deconvoluterUFSA_precursorType_correctorxlsx2msp

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Fragmentation Spectra Annotatorfragmentation_spectra_annotator
aggregation method for FSAFSA_aggregate
FSA annotation text repelFSA_annotation_text_repel
FSA_dir.createFSA_dir.create
FSA FSdb xlsx AnalyzerFSA_FSdb_xlsxAnalyzer
FSA loadRdataFSA_loadRdata
FSA Locate regexFSA_locate_regex
FSA logRecorderFSA_logRecorder
FSA messageFSA_message
FSA msp annotatorFSA_msp_annotator
FSA Cytoscape Files GeneratorFSA_msp2Cytoscape
plot FSdb to SpectraFSA_plotFSdb2Spectra
aggregate function for IDSL.FSAFSA_R.aggregate
FSA Spectra Marker GeneratorFSA_spectra_marker_generator
FSA SpectraSimilarity xlsx AnalyzerFSA_SpectraSimilarity_xlsxAnalyzer
FSA Unique MSP Block TaggerFSA_uniqueMSPblockTagger
FSA_uniqueMSPblockTaggerUntargetedFSA_uniqueMSPblockTaggerUntargeted
FSA workflowFSA_workflow
FSA xlsx AnalyzerFSA_xlsxAnalyzer
FSdb file generatorFSdb_file_generator
FSdb subsetterFSdb_subsetter
Fragmentation Spectra DataBase (FSDB) to MSPFSdb2msp
FSdb2PeakXcolSubsetterFSdb2PeakXcolSubsetter
Precursor Types from Fragmentation Spectra DataBase (FSDB)FSdb2precursorType
MGF to MSPmgf2msp
msp to Fragmentation Spectra DataBase (FSDB)msp2FSdb
msp to Fragmentation Spectra DataBase (FSDB)msp2TrainingMatrix
MSP Pos/Neg SplittermspPosNegSplitter
plot spectra from FSdb coreplotFSdb2SpectraCore
Mixer 1:1 spectra A and Bspectra_1A1B_mixer
Spectra Integratorspectra_integrator
Spectra Ion Filterspectra_ion_filter
Spectral Entropy Calculatorspectral_entropy_calculator
Spectral Entropy Calculatorspectral_entropy_similarity_score
Example for a stacked spectrastackedSpectra
Element SorterUFSA_element_sorter
Molecular Formula Vector GeneratorUFSA_formula_vector_generator
Print Hill Molecular FormulaUFSA_hill_molecular_formula_printer
Ionization Pathway DeconvoluterUFSA_ionization_pathway_deconvoluter
UFA Precursor Type CorrectorUFSA_precursorType_corrector
xlsx to MSPxlsx2msp