Files in shubham1637/DIAlign
Dynamic Programming Based Alignment of MS2 Chromatograms
.Rbuildignore
.dockerignore
.gitignore
.travis.yml
CMakeLists.txt
DESCRIPTION
DIAlignR.Rproj
Dockerfile
NAMESPACE
NEWS
R/DIAlignR.R
R/RcppExports.R
R/affine_aligned_obj.R
R/align_dia_runs.R
R/chromatogram_manip.R
R/data.R
R/fill_missing_intensity.R
R/get_analytes.R
R/get_filenames.R
R/get_global_fit.R
R/get_osw_query.R
R/get_peaks_chromatograms.R
R/merge_chromatogram.R
R/merge_order.R
R/merge_osw_mzml.R
R/merge_runs.R
R/mstAlign.R
R/nature_paper.R
R/pairwise_pep_peak_corp.R
R/peak_area.R
R/post_alignment.R
R/progressive_alignment.R
R/pyopenms.R
R/read_mzml.R
R/read_osw.R
R/reduce_files.R
R/scripts.R
R/sqMass.R
R/utils.R
R/visualise_chromatograms.R
README.md
Rscript/alignTargetedRuns_cli.R
TODO
data-raw/test_GenerateChroms.txt
data-raw/test_GenerateData.R
data/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.rda
data/alignObj_DIAlignR.rda
data/masterXICs_DIAlignR.rda
data/multipeptide_DIAlignR.rda
data/oswFiles_DIAlignR.rda
inst/buildDIAlignR.txt
inst/extdata/osw/merged.osw
inst/extdata/xics/hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt.chrom.mzML
inst/extdata/xics/hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt.chrom.sqMass
inst/extdata/xics/hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
inst/extdata/xics/hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.sqMass
inst/extdata/xics/hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
inst/extdata/xics/hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.sqMass
inst/metabo/osw/merged.osw
inst/metabo/xics/PestMix1_8Step1Plasma1SWATH20-50.chrom.mzML
inst/metabo/xics/PestMix1_8Step1Plasma1SWATH20-50.chrom.sqMass
inst/metabo/xics/PestMix1_8Step8Plasma1SWATH20-50.chrom.mzML
inst/metabo/xics/PestMix1_8Step8Plasma1SWATH20-50.chrom.sqMass
inst/ptms/osw/merged.osw
inst/ptms/xics/chludwig_K150309_004b_SW_1_16.chrom.sqMass
inst/ptms/xics/chludwig_K150309_008_SW_1_4.chrom.sqMass
inst/ptms/xics/chludwig_K150309_013_SW_0.chrom.sqMass
man/AffineAlignObj-class.Rd
man/AffineAlignObjLight-class.Rd
man/AffineAlignObjMedium-class.Rd
man/AlignObj-class.Rd
man/DIAlignR.Rd
man/MSTperBatch.Rd
man/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.Rd
man/addFlankToLeft.Rd
man/addFlankToRight.Rd
man/addXIC.Rd
man/alignChromatogramsCpp.Rd
man/alignObj_DIAlignR.Rd
man/alignTargetedRuns.Rd
man/alignToMaster.Rd
man/alignToRef.Rd
man/alignToRefMST.Rd
man/alignToRoot4.Rd
man/alignedXIC.Rd
man/alignmentStats.Rd
man/analytesFromFeatures.Rd
man/approxFill.Rd
man/areaIntegrator.Rd
man/as.list-AffineAlignObj-method.Rd
man/as.list-AffineAlignObjLight-method.Rd
man/as.list-AffineAlignObjMedium-method.Rd
man/as.list-AlignObj-method.Rd
man/blobXICs.Rd
man/calculateIntensity.Rd
man/checkOverlap.Rd
man/checkParams.Rd
man/childXIC.Rd
man/childXICs.Rd
man/chromatogramIdAsInteger.Rd
man/constrainSimCpp.Rd
man/createMZML.Rd
man/createSqMass.Rd
man/dialignrLoess.Rd
man/doAffineAlignmentCpp.Rd
man/doAlignmentCpp.Rd
man/extractXIC_group.Rd
man/extractXIC_group2.Rd
man/fetchAnalytesInfo.Rd
man/fetchFeaturesFromRun.Rd
man/fetchPeptidesInfo.Rd
man/fetchPeptidesInfo2.Rd
man/fetchPrecursorsInfo.Rd
man/fetchTransitionsFromRun.Rd
man/filenamesFromMZML.Rd
man/filenamesFromOSW.Rd
man/getAlignObj.Rd
man/getAlignObjs.Rd
man/getAlignedFigs.Rd
man/getAlignedIndices.Rd
man/getAlignedTimes.Rd
man/getAlignedTimesCpp.Rd
man/getAlignedTimesFast.Rd
man/getAnalytesQuery.Rd
man/getBaseGapPenaltyCpp.Rd
man/getChildFeature.Rd
man/getChildXICpp.Rd
man/getChildXICs.Rd
man/getChromSimMatCpp.Rd
man/getChromatogramIndices.Rd
man/getFeatures.Rd
man/getFeaturesQuery.Rd
man/getGlobalAlignMaskCpp.Rd
man/getGlobalAlignment.Rd
man/getGlobalFits.Rd
man/getLOESSfit.Rd
man/getLinearfit.Rd
man/getMST.Rd
man/getMZMLpointers.Rd
man/getMappedRT.Rd
man/getMultipeptide.Rd
man/getNativeIDs.Rd
man/getNodeIDs.Rd
man/getNodeRun.Rd
man/getOswAnalytes.Rd
man/getOswFiles.Rd
man/getPeptideQuery.Rd
man/getPeptideQuery2.Rd
man/getPeptideScores.Rd
man/getPrecursorByID.Rd
man/getPrecursorIndices.Rd
man/getPrecursorSubset.Rd
man/getPrecursors.Rd
man/getPrecursorsQuery.Rd
man/getPrecursorsQueryID.Rd
man/getQuery.Rd
man/getRSE.Rd
man/getRTdf.Rd
man/getRefExpFeatureMap.Rd
man/getRefRun.Rd
man/getRunNames.Rd
man/getSeqSimMatCpp.Rd
man/getTransitions.Rd
man/getTransitionsQuery.Rd
man/getTree.Rd
man/getXICs.Rd
man/getXICs4AlignObj.Rd
man/get_ropenms.Rd
man/imputeChromatogram.Rd
man/ipfReassignFDR.Rd
man/mapIdxToTime.Rd
man/mapPrecursorToChromIndices.Rd
man/mappedRTfromAlignObj.Rd
man/masterXICs_DIAlignR.Rd
man/mergeOswAnalytes_ChromHeader.Rd
man/mergeXIC.Rd
man/mstAlignRuns.Rd
man/mstScript1.Rd
man/mstScript2.Rd
man/multipeptide_DIAlignR.Rd
man/nrDesc.Rd
man/oswFiles_DIAlignR.Rd
man/otherChildXICpp.Rd
man/paramsDIAlignR.Rd
man/perBatch.Rd
man/pickNearestFeature.Rd
man/plotAlignedAnalytes.Rd
man/plotAlignmentPath.Rd
man/plotAnalyteXICs.Rd
man/plotSingleAlignedChrom.Rd
man/plotXICgroup.Rd
man/populateReferenceExperimentFeatureAlignmentMap.Rd
man/progAlignRuns.Rd
man/progComb3.Rd
man/progSplit2.Rd
man/progSplit4.Rd
man/progTree1.Rd
man/readMzMLHeader.Rd
man/readSqMassHeader.Rd
man/recalculateIntensity.Rd
man/reduceXICs.Rd
man/script1.Rd
man/script2.Rd
man/setAlignmentRank.Rd
man/sgolayCpp.Rd
man/sgolayFill.Rd
man/smoothSingleXIC.Rd
man/smoothXICs.Rd
man/splineFill.Rd
man/splineFillCpp.Rd
man/traverseDown.Rd
man/traverseMST.Rd
man/traverseUp.Rd
man/trfrParentFeature.Rd
man/trimXICs.Rd
man/uncompressVec.Rd
man/updateFileInfo.Rd
man/updateOnalignTargetedRuns.Rd
man/writeOutFeatureAlignmentMap.Rd
man/writeTables.Rd
python/DIAlignPy/DIAlign.pxd
python/DIAlignPy/PyDIAlign.pyx
python/DIAlignPy/README.md
python/DIAlignPy/setup.py
python/DIAlignPy/test_data.py
python/DIAlignPy/test_pydialign.py
python/scripts/DIAlignR4win.py
snakemake/Snakefile.dialignr
snakemake/cmd.sh
src/ChromatogramPeak.cpp
src/ChromatogramPeak.h
src/CppInterface.hpp
src/DPosition.cpp
src/DPosition.h
src/MSChromatogram.cpp
src/MSChromatogram.h
src/PeakIntegrator.cpp
src/PeakIntegrator.h
src/RcppExports.cpp
src/Rmain.cpp
src/SavitzkyGolayFilter.cpp
src/SavitzkyGolayFilter.h
src/affinealignment.cpp
src/affinealignment.h
src/affinealignobj.cpp
src/affinealignobj.h
src/alignment.cpp
src/alignment.h
src/chromSimMatrix.cpp
src/chromSimMatrix.h
src/constrainMat.cpp
src/constrainMat.h
src/doc/Doxyfile
src/doc_pages/Initialization.md
src/doc_pages/Matrices.md
src/doc_pages/mainpage.md
src/doc_pages/nonoverlap.svg
src/doc_pages/overlap.svg
src/gapPenalty.cpp
src/gapPenalty.h
src/integrateArea.cpp
src/integrateArea.h
src/interface.cpp
src/interface.h
src/miscell.cpp
src/miscell.h
src/peakIntegration/README.txt
src/peakIntegration/test.cpp
src/run_alignment.cpp
src/similarityMatrix.h
src/simpleFcn.cpp
src/simpleFcn.h
src/spline.cpp
src/spline.h
src/test/test_affinealignment.cpp
src/test/test_affinealignobj.cpp
src/test/test_alignment.cpp
src/test/test_chromSimMatrix.cpp
src/test/test_constrainMat.cpp
src/test/test_gapPenalty.cpp
src/test/test_integrateArea.cpp
src/test/test_large.tsv
src/test/test_miscell.cpp
src/test/test_simpleFcn.cpp
src/test/test_small.tsv
src/test/test_utils.cpp
src/utils.cpp
src/utils.h
tests/testthat.R
tests/testthat/test.tsv
tests/testthat/test2.tsv
tests/testthat/test3.tsv
tests/testthat/test4.tsv
tests/testthat/test5.tsv
tests/testthat/test6.tsv
tests/testthat/test7.tsv
tests/testthat/test_Rmain.R
tests/testthat/test_align_dia_runs.R
tests/testthat/test_chromatogram_manip.R
tests/testthat/test_fill_missing_intensity.R
tests/testthat/test_get_analytes.R
tests/testthat/test_get_filenames.R
tests/testthat/test_get_global_fit.R
tests/testthat/test_get_osw_query.R
tests/testthat/test_get_peaks_chromatograms.R
tests/testthat/test_merge_chromatogram.R
tests/testthat/test_merge_order.R
tests/testthat/test_merge_osw_mzml.R
tests/testthat/test_merge_runs.R
tests/testthat/test_metabo.tsv
tests/testthat/test_mstAlign.R
tests/testthat/test_pairwise_pep_peak_corp.R
tests/testthat/test_peak_area.R
tests/testthat/test_post_alignment.R
tests/testthat/test_progressive_alignment.R
tests/testthat/test_pyopenms.R
tests/testthat/test_read_mzml.R
tests/testthat/test_read_osw.R
tests/testthat/test_sqMass.R
tests/testthat/test_utils.R
vignettes/DIAlignR-vignette.R
vignettes/DIAlignR-vignette.Rmd
vignettes/DIAlignR-vignette.html
vignettes/DIAlignR.bib
