d5f226b48118ad28f04e5a443b823dc7 *DESCRIPTION
a8496ee9130d4b2ebe0bb3c507f20d24 *NAMESPACE
4e10982d09f2c2d46a83eb3e6e51d669 *R/ExpressionAnalysis.R
d135733f76cfb43b77461cc2f97532e3 *R/Graphics.R
5a95cc6f1b7c1377ba3068a6effeb234 *R/IdentificationAnalysis.R
8b503608f4fdefeb5a101896460bd3d2 *R/Parser.R
8ea74c46c729b00e42310ae4a82f717c *R/SafeQuantAnalysis.R
797c2163e5cf8782dbc4e79908c4c71c *R/TMT.R
8fa20ca06a6456f085114da17ac5f3b0 *R/UserOptions.R
485e7476568544ef6d6801cea8c9636b *README.md
213129760f9b98506bfa4901fc647ca8 *exec/filterLargeProgenesisPeptideFile.pl
658119e29673ffafd63ee8236f17ef57 *exec/installDependencies.R
2e46fd29fd20fecc9c955a04dad2f648 *exec/roxygenize.R
f6afeee924ac48179570ce737284b112 *exec/safeQuant.R
beaf5b1028a569e4c03ae5a39b04f6b4 *inst/manuals/SafeQuant-man.pdf
1404e5d260a240e1b718e50aab5b06c8 *inst/manuals/SafeQuant_UseCases.txt
3380d17981b26dd83a7853183a74ae52 *inst/manuals/tsv_spreadsheet_help.docx
aac3ce5613cc0f7f4fe4e904f34986c9 *inst/manuals/tsv_spreadsheet_help.pdf
e0f50b272efe9b65fccb8a6fde8a295e *man/COLORS.Rd
db182fd3806ee793dabae65c1eb65328 *man/addIdQvalues.Rd
f4964a03d399fc0bff26129a04016f89 *man/addScaffoldPTMFAnnotations.Rd
8154e563883874ec85261255367fedc5 *man/barplotMSSignal.Rd
c5920dc8e5a2e9c2867d37db17879def *man/createExpDesign.Rd
c5e34b2ed0068059fe199028ebb9cd0d *man/createExpressionDataset.Rd
35dfab3fd0f2de4749bb91fcef34f2a3 *man/createPairedExpDesign.Rd
518736077db67320f73d10395811eebd *man/cvBoxplot.Rd
d075ea7611574e96baa00d9dfac3c588 *man/expDesignTagToExpDesign.Rd
9ae49d6b1a760c6175759e01f8d5130b *man/export.Rd
44cd5aeba295f2a022ac794ba92f3ee3 *man/getAAProteinCoordinates.Rd
3ec6985c4a93c9569c1ab6c8663f57b2 *man/getAllCV.Rd
931b83099aa29185f474eb455cff50b0 *man/getAllEBayes.Rd
f352826b91c24a93f14109e363e6c2b3 *man/getBaselineIntensity.Rd
fe10e804dc8f3f80e2bdea76bc177c73 *man/getCV.Rd
f9abc5fbe69de124693699c8401b2990 *man/getExpDesignProgenesisCsv.Rd
86d085278160539ab9e44770feb541f9 *man/getGlobalNormFactors.Rd
d0d1799324a3bbc49ac538090f0e289f *man/getIBAQEset.Rd
c7b16ee75f64c77c01e9d3f018eae47f *man/getIdLevelQvals.Rd
080e34676f3b3d4276c5d266fe81269c *man/getImpuritiesMatrix.Rd
ea8fc4be35bf15067409fbea9ca04118 *man/getIntSumPerProtein.Rd
db7f4c5eefe96996becb743b39ada9bd *man/getLoocvFoldError.Rd
e96ffc2611614de691c803dd8cf8df2c *man/getMaxIndex.Rd
6ec411c89ea1fa05200fb16409f1fec7 *man/getMeanCenteredRange.Rd
c398c6fa9c3213578e8a473c4833d5b0 *man/getModifProteinCoordinates.Rd
37e305f70153576ab6c081116cc5fc86 *man/getMotifX.Rd
38859c7d3f152ff44c90a8606b414caa *man/getNbDetectablePeptides.Rd
ccc34b1fd74d1f977c21611a935411ae *man/getNbMisCleavages.Rd
52e0fe26bf46be6d0362199ad6e6a225 *man/getNbPeptidesPerProtein.Rd
9040cf5c6a403167ffd511d47a17bc66 *man/getNbSpectraPerProtein.Rd
75eee4054f07474ac60737f2341ee033 *man/getPeptides.Rd
b4feabfae03368f0160956dfd0c870eb *man/getRTNormFactors.Rd
e6f8231f4926c20f38e44e2349f1399f *man/getRatios.Rd
3e34d8bcd186bbd4dbde61bd94043078 *man/getScoreCutOff.Rd
8f76560b38b8ed08bc92c56f33f676b9 *man/getSignalPerCondition.Rd
ac7c022bc4bc851226d0451f50436dc3 *man/getTopX.Rd
88c252f670b692855b52ba939ee35d14 *man/getUserOptions.Rd
3f1d6e5685ac801ffbea5bae5913da89 *man/globalNormalize.Rd
99d2d9955feb50f2de54371e1b29f05f *man/hClustHeatMap.Rd
c0a777f78e5a73b61343ddc225312c84 *man/isCon.Rd
9d8e498f679824bd8e49c101a240c611 *man/isDecoy.Rd
d2661517543216beb74ed93f0366ca1e *man/isStrippedACs.Rd
ca77a761fda96d3d17d176d845b39b88 *man/maPlotSQ.Rd
69c295a8585a73bb8f4f63f7ea39ce50 *man/missinValueBarplot.Rd
3f62ed400d15d786d3eb5b2e603c38cb *man/option_list.Rd
21faa7c77c899d3aba7b4de4fa7b8e8d *man/pairsAnnot.Rd
dc0b43cad537c20538bf1f23bc285910 *man/parseMaxQuantProteinGroupTxt.Rd
6eee1ac15d430a3b66ade833437c21c5 *man/parseProgenesisFeatureCsv.Rd
cf762cafbc40f4117a0c76a9221581bf *man/parseProgenesisPeptideMeasurementCsv.Rd
dc7ef04500af38cdb9aa483208913034 *man/parseProgenesisProteinCsv.Rd
b1a47c902864c79e824fcf91811379b9 *man/parseScaffoldPTMReport.Rd
a3db382d14f2c384038004d7dc6a481d *man/parseScaffoldRawFile.Rd
31312c8449c6db4f7319cd52170b9dec *man/perFeatureNormalization.Rd
71e9c51c7e9253967b37f3ae94003127 *man/plotAbsEstCalibrationCurve.Rd
169e1cb7b823967ec1d0e7f235aaa059 *man/plotAdjustedVsNonAdjustedRatio.Rd
5830bd326d633efaded9a806a9e474a4 *man/plotExpDesign.Rd
181208afb0ad96f97c3c68f3677e9de4 *man/plotIdScoreVsFDR.Rd
5c37bd3aadf957d182b5d63a694c4440 *man/plotMSSignalDistributions.Rd
3fc9699a16bb7f68a0dc681e2272ebdf *man/plotNbIdentificationsVsRT.Rd
1daa67ffc6a0b44ef7f0e0558cdf8499 *man/plotNbValidDeFeaturesPerFDR.Rd
03f4524cf7380270bac732e50da4d0d7 *man/plotPrecMassErrorDistrib.Rd
46ef183073d4583f8184d99d61d9c163 *man/plotPrecMassErrorVsScore.Rd
1d8b3e78b090fee0a3c6e943fc2e42d0 *man/plotQValueVsPValue.Rd
0f60d53652cf36832c31c777bc9d3c13 *man/plotROC.Rd
977d513f5c7bb0eda4e05eb8be9d3889 *man/plotRTNorm.Rd
1e98856ded6bb3878a4ad04cedebaff3 *man/plotRTNormSummary.Rd
7d9f64d17a9136e008a3188182847d11 *man/plotScoreDistrib.Rd
b42dfe7868cab6a4eb3d2b6f151c10bb *man/plotVolcano.Rd
2b9b38422f8eb0a574d19d690d956381 *man/plotXYDensity.Rd
39f486099b7bf4c1129011a8d564890f *man/purityCorrectTMT.Rd
eb42825306dfb74e92f63fa240b543e9 *man/removeOutliers.Rd
338ba670972cac27efb0a1a4b865d068 *man/rollUp.Rd
959de25ec44bb5e2025711a015f230ef *man/rtNormalize.Rd
07e1ba8a096863ae3f59ec8acf1838ce *man/safeQuantAnalysis.Rd
a13a3313c6fa904b33f0efb84b6a3766 *man/setNbPeptidesPerProtein.Rd
5553d0d0d14c1f1ce0dba02f9c58e969 *man/setNbSpectraPerProtein.Rd
fb38520c2ac463b6ae0c0e30f74fc161 *man/sqNormalize.Rd
7eaa30ae02b06d95d4e7e4e48072c325 *man/standardise.Rd
b2bb8cf143d9c4c755beeacafe3c5622 *man/stripACs.Rd
c91f969f3174041a5b04f5c4a5e5896a *tests/initTestSession.R
f7dd8697217a164c8a84f6e3bd2d7efd *tests/runAllTest.R
a9307f535221d6333b4220b2a8a2796b *tests/testData/SQ_Results/SQ_Results.pdf
acd7834db15f3ad351625bca1b46abb5 *tests/testData/SQ_Results/SQ_Results_PROTEIN.tsv
0affd235e2bc41ffbaf205bc9d1c506a *tests/testData/SQ_Results/SQ_Results_SQ_PARAMS.TXT
9fe5bf6277ed2479e7c065d41de41e25 *tests/testData/maxquant_protein_groups.csv
de790864ecb586f50b210eb56f7dbb75 *tests/testData/mouse_proteins.fasta
cce2ed2238d94c80eb5454cb5b06f20c *tests/testData/progenesis_feature_export1.csv
aff1995b357c4f89a2cbdd33d3f7db65 *tests/testData/progenesis_pep_measurement1.csv
a5f6cc1ca2638c70e16ca815624faab4 *tests/testData/progenesis_pep_measurement_fractionated1.csv
72e07b658499d2bb327ab3b175b4a938 *tests/testData/progenesis_protein_export1.csv
5708a62320c3421599444f5a7d155751 *tests/testData/scaffoldPtm_spectrum_report.xls
f45977d644696deb5c60844a44de3784 *tests/testData/scaffold_tmt10plex_calibMix_raw.xls
674e8d39d64ac48b7b91adec99724cda *tests/testData/scaffold_tmt10plex_raw.xls
c082dff4708ee54f3e86ad1f9ae540cd *tests/testData/scaffold_tmt10plex_raw_phospho.xls
43601181a3efe34f68d292e14c4afdf7 *tests/testData/scaffold_tmt6plex_raw.xls
18004e1847b7e93e666482711364b0fa *tests/testData/skyline_transition_results.csv
15b76dc38040feceaf66892cd607c3b8 *tests/testExpressionAnalysis.R
8781b930d4f1900f9098f7a2747b7657 *tests/testGraphics.R
f553d6c347481f067df7bc6bc567e3ad *tests/testIdentificationAnalysis.R
f5079ad81c4581a5f94273bae514e735 *tests/testParser.R
ca88e7ee508e291ccd78d42016d8a5a8 *tests/testSafeQuantAnalysis.R
f14ba9a0d0239317ba38ca982995e0ec *tests/testTMT.R
f130d7a9cb3bc7d3d0bd4abf7bd3b077 *tests/testUserOptions.R
