Files in xia-lab/OptiLCMS

Optimized LC-MS Spectra Processing

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/C_function.R R/Global_setting.R R/MSn_processing.R R/OptiLCMS_Class.R R/Optimize_params.R R/Other_Utils.R R/Params_db.R R/Perform_functions.R R/ROI_Extraction.R R/RcppExports.R R/Resume_functions.R R/Spectra_Utils.R R/Spectra_import.R R/Spectra_visulization.R R/autoconfig.R README.md

data/mSet.rda

inst/CITATION

inst/hmdb/hmdb_all.rds

inst/lists/ions.csv

inst/lists/neutraladdition.csv

inst/lists/neutralloss.csv

inst/rules/extended_adducts_neg.csv

inst/rules/extended_adducts_pos.csv

inst/rules/primary_adducts_neg.csv

inst/rules/primary_adducts_pos.csv

inst/script/Example_Running_Script.R man/CentroidCheck.Rd man/CentroidMSData.Rd man/ExecutePlan.Rd man/Export.Annotation.Rd man/Export.PeakSummary.Rd man/Export.PeakTable.Rd man/FormatMSnAnnotation.Rd man/FormatPeakList.Rd man/GaussModel.Rd man/ImportRawMSData.Rd man/InitDataObjects.Rd man/InitializaPlan.Rd man/OptiLCMS.Rd man/PerformDBSearchingBatch.Rd man/PerformDDADeconvolution.Rd man/PerformDIADeconvolution.Rd man/PerformDataInspect.Rd man/PerformDataTrimming.Rd man/PerformMSnImport.Rd man/PerformMirrorPlotting.Rd man/PerformParamsOptimization.Rd man/PerformPeakAlignment.Rd man/PerformPeakAnnotation.Rd man/PerformPeakFiling.Rd man/PerformPeakPicking.Rd man/PerformPeakProfiling.Rd man/PerformROIExtraction.Rd man/PerformResultsExport.Rd man/PerformSpectrumConsenus.Rd man/PlotSpectraBPIadj.Rd man/PlotSpectraInsensityStistics.Rd man/PlotSpectraPCA.Rd man/PlotSpectraRTadj.Rd man/PlotXIC.Rd man/SetAnnotationParam.Rd man/SetGlobalParallel.Rd man/SetPeakParam.Rd man/SetPlotParam.Rd man/UpdateRawfiles.Rd man/calculate_entropy_similarity.Rd man/calculate_unweighted_entropy_similarity.Rd man/mSet.Rd man/plotBPIs.Rd man/plotMSfeature.Rd man/plotSingleTIC.Rd man/plotTICs.Rd man/running.plan.Rd man/updateRawSpectraPath.Rd

src/CleanSpectrum.c

src/CleanSpectrum.h

src/DecoSpectra.cpp

src/DecoSpectra.h

src/DetectPeaks.cpp

src/DetectPeaks.h

src/Makevars

src/Makevars.win

src/PerformDDAProcess.cpp

src/PerformDDAProcess.h

src/PerformDIAProcess.cpp

src/PerformDIAProcess.h

src/RcppExports.cpp

src/SWATH_DIA_Deconv.cpp

src/SpectralEntropy.c

src/SpectralEntropy.h

src/binarySearch.h

src/dda_utilities.cpp

src/dda_utilities.h

src/decorana.f

src/entropy.cpp

src/entropy.h

src/export_interfece.cpp

src/fastMatch.c

src/fastMatch.h

src/fastcluster.h

src/hclust_ultrafast.cpp

src/hclust_ultrafast.h

src/init.c

src/linear_regression.cpp

src/linear_regression.h

src/lowess.cpp

src/lowess.h

src/massifquant/DataKeeper.cpp

src/massifquant/DataKeeper.h

src/massifquant/OpOverload.cpp

src/massifquant/OpOverload.h

src/massifquant/SegProc.cpp

src/massifquant/SegProc.h

src/massifquant/TrMgr.cpp

src/massifquant/TrMgr.h

src/massifquant/Tracker.cpp

src/massifquant/Tracker.h

src/massifquant/dpq.h

src/massifquant/nmath.h

src/massifquant/xcms_massifquant.cpp

src/mzROI.c

src/obiwarp/lmat.h

src/obiwarp/mat.cpp

src/obiwarp/mat.h

src/obiwarp/vec.cpp

src/obiwarp/vec.h

src/obiwarp/xcms_dynprog.cpp

src/obiwarp/xcms_dynprog.h

src/obiwarp/xcms_lmat.cpp

src/optim_src.h

src/optim_ultra.cpp

src/optim_ultra.h

src/pense/alias.hpp

src/pense/autoconfig.hpp

src/pense/cd_pense.hpp

src/pense/constants.hpp

src/pense/container_utility.hpp

src/pense/enpy_initest.cc

src/pense/enpy_initest.hpp

src/pense/enpy_psc.cc

src/pense/enpy_psc.hpp

src/pense/enpy_types.hpp

src/pense/m_loss.hpp

src/pense/nsoptim.hpp

src/pense/nsoptim/armadillo.hpp

src/pense/nsoptim/armadillo_forward.hpp

src/pense/nsoptim/config.hpp

src/pense/nsoptim/container.hpp

src/pense/nsoptim/container/data.hpp

src/pense/nsoptim/container/forward.hpp

src/pense/nsoptim/container/metrics.hpp

src/pense/nsoptim/container/regression_coefficients.hpp

src/pense/nsoptim/objective.hpp

src/pense/nsoptim/objective/adaptive_en_penalty.hpp

src/pense/nsoptim/objective/convex.hpp

src/pense/nsoptim/objective/en_penalty.hpp

src/pense/nsoptim/objective/forward.hpp

src/pense/nsoptim/objective/loss.hpp

src/pense/nsoptim/objective/ls_regression_loss.hpp

src/pense/nsoptim/objective/penalty.hpp

src/pense/nsoptim/optimizer.hpp

src/pense/nsoptim/optimizer/admm.hpp

src/pense/nsoptim/optimizer/auglars.hpp

src/pense/nsoptim/optimizer/coordinate_descent.hpp

src/pense/nsoptim/optimizer/dal.hpp

src/pense/nsoptim/optimizer/dal_helper.hpp

src/pense/nsoptim/optimizer/linear_algebra_utilities.hpp

src/pense/nsoptim/optimizer/mm.hpp

src/pense/nsoptim/optimizer/optimizer_base.hpp

src/pense/nsoptim/optimizer/optimum.hpp

src/pense/nsoptim/optimizer/soft_threshold.hpp

src/pense/nsoptim/rcpp_integration.hpp

src/pense/nsoptim/traits/can_evaluate.hpp

src/pense/nsoptim/traits/can_optimize.hpp

src/pense/nsoptim/traits/has_convex_surrogate.hpp

src/pense/nsoptim/traits/has_difference_op.hpp

src/pense/nsoptim/traits/is_adaptive.hpp

src/pense/nsoptim/traits/is_differentiable.hpp

src/pense/nsoptim/traits/is_en_penalty.hpp

src/pense/nsoptim/traits/is_iterative_algorithm.hpp

src/pense/nsoptim/traits/is_loss_function.hpp

src/pense/nsoptim/traits/is_ls_regression_loss.hpp

src/pense/nsoptim/traits/is_penalty_function.hpp

src/pense/nsoptim/traits/is_weighted.hpp

src/pense/nsoptim/traits/sfinae_types.hpp

src/pense/nsoptim/traits/traits.hpp

src/pense/nsoptim/utilities.hpp

src/pense/nsoptim_forward.hpp

src/pense/omp_utils.hpp

src/pense/r_en_regression.cc

src/pense/r_en_regression.hpp

src/pense/r_enpy.cc

src/pense/r_enpy.hpp

src/pense/r_interface.cc

src/pense/r_interface_utils.cc

src/pense/r_interface_utils.hpp

src/pense/r_mesten_regression.cc

src/pense/r_mesten_regression.hpp

src/pense/r_pense_regression.cc

src/pense/r_pense_regression.hpp

src/pense/r_robust_utils.cc

src/pense/r_robust_utils.hpp

src/pense/r_utilities.cc

src/pense/r_utilities.hpp

src/pense/rcpp_integration.hpp

src/pense/rcpp_parse_config.cc

src/pense/rcpp_parse_config.hpp

src/pense/rcpp_utils.hpp

src/pense/rcpp_utils_forward.hpp

src/pense/regularization_path.hpp

src/pense/regularization_path_new.hpp

src/pense/rho.cc

src/pense/rho.hpp

src/pense/robust_scale_location.cc

src/pense/robust_scale_location.hpp

src/pense/s_loss.hpp

src/rules.h

src/spectra_searching.cpp

src/spectrumConsensus.cpp

src/sqlite/shell.c

src/sqlite/sqlite3.c

src/sqlite/sqlite3.h

src/sqlite/sqlite3ext.h

src/sqlite_utilities.cpp

src/sqlite_utilities.h

src/util.cpp

src/utilities.cpp

src/utilities.h

src/xcms_binners.c

src/xcms_binners.h

src/xcms_obiwarp.cpp

vignettes/OptiLCMS_MS1.Rmd

xia-lab/OptiLCMS documentation built on March 27, 2024, 11:11 a.m.