Files in michaelwitting/masstrixR
Annotation of MS based metabolomics data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/MS1_AdductDbCreate.R
R/MS1_AdductDbSearch.R
R/MS1_IsotopePattern.R
R/MS1_Utilities.R
R/MS1_isotopePattern.R
R/MS2_LibraryReader.R
R/MS2_SpectrumDbCreate.R
R/MS2_SpectrumDbSearch.R
R/MS2_Utilities.R
R/MS2_specSimilarty.R
R/Utils_ParseAgilent.R
R/Utils_ParseGenedata.R
R/Utils_SpectraImportExport.R
R/Utils_TidyFunctions.R
R/Utils_plotting.R
R/Utils_spectrumFunctions.R
README.md
data/isotopes.rda
inst/extdata/databases/chebi_20190125.txt
inst/extdata/databases/hmdb_20190125.txt
inst/extdata/databases/lipidMaps_20190125.txt
inst/extdata/databases/wormJam_20190613.txt
inst/extdata/databases/ymdb_20190125.txt
inst/extdata/exampleData/Celegans_lipids_ms2/ceramides.mgf
inst/extdata/exampleData/Celegans_lipids_ms2/wormLipidDb_MS2.sqlite
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000101.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000201.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000202.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000301.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000302.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000303.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000401.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000402.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000403.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000501.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000502.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000503.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000601.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000602.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000603.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000701.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000702.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000703.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000801.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000802.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000803.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000901.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000902.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP000903.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP001001.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP001002.txt
inst/extdata/exampleData/Celegans_ms2/MassBankRecords/RP001003.txt
inst/extdata/exampleData/Celegans_ms2/exampleMs2.mgf
inst/extdata/exampleData/Celegans_mz/NaAcHILICPos_Cluster.gda
inst/extdata/exampleData/Celegans_mz_rt/peakTable.txt
inst/extdata/exampleData/Celegans_mz_rt/rtidb.txt
inst/extdata/exampleData/databases/example_pos_MH_MNa.sqlite
inst/extdata/exampleData/databases/ymdb_example.txt
inst/extdata/exampleData/listFormats/Agilent_CEF.cef
inst/testdata/test_db_creation_ms1_ymdb_example.txt
inst/testdata/test_utilities_MS2_AutoMSn_CelegansLipids.mgf
inst/testdata/test_utilities_MS2_wormLipidDb_MS2.sqlite
man/alignSpectra.Rd
man/bin_Spectra.Rd
man/bin_Spectrum.Rd
man/calculateKendrickMass.Rd
man/calculateKendrickMassDefect.Rd
man/calculateNominalKendrickMass.Rd
man/calculateRefKendrickMassDefect.Rd
man/checkRmkd.Rd
man/cleanSpectra.Rd
man/clean_spectrum.Rd
man/commonPeaks.Rd
man/common_peaks.Rd
man/containsFragmentDifference.Rd
man/containsNeutralLossIon.Rd
man/containsProductIon.Rd
man/contains_fragment_diff.Rd
man/contains_neutral_loss.Rd
man/contains_product_ion.Rd
man/createDb.Rd
man/createMs2Db.Rd
man/createResultsSet.Rd
man/create_results_set.Rd
man/dot-bin_values.Rd
man/dot-dotproduct.Rd
man/dot-fix_breaks.Rd
man/filterIsotopePeaks.Rd
man/forwardDotProduct.Rd
man/forward_dotproduct.Rd
man/ionFormulaSearch.Rd
man/isoPatternSimilarity.Rd
man/matchMassDiff.Rd
man/match_mz_inter.Rd
man/match_mz_intra.Rd
man/mzSearch.Rd
man/neutralFormulaSearch.Rd
man/predictIsoPattern.Rd
man/prepareCompoundList.Rd
man/readAnnotatedMgfData.Rd
man/readGdaFile.Rd
man/readMassBankFile.Rd
man/readMassBankFolder.Rd
man/reconstructIsoPattern.Rd
man/reverseDotProduct.Rd
man/reverse_dotproduct.Rd
man/scoreIsoPattern.Rd
man/searchByPrecursor.Rd
man/search_by_precursor.Rd
man/validateCompoundList.Rd
masstrixR.Rproj
tests/setup_utilities_ms2.R
tests/test_utilities_ms2.R
tests/testthat/test_ion_matching.R
vignettes/example_MS2.sqlite
vignettes/example_isoLabel_pos_MH_MNa.sqlite
vignettes/example_pos_MH_MNa.sqlite
vignettes/example_pos_MH_MNa_withRT.sqlite
vignettes/masstrixR_createSQLiteDB_MS1.Rmd
vignettes/masstrixR_createSQLiteDB_MS2.Rmd
vignettes/masstrixR_ms2Functions.Rmd
vignettes/masstrixR_ms2Matching.Rmd
vignettes/masstrixR_mzCcsMatching.Rmd
vignettes/masstrixR_mzMatching.Rmd
vignettes/masstrixR_mzRtMatching.Rmd
