d2293b091d9788cb852ce96999faae45 *DESCRIPTION
885c4037637d73ec37afe886f6e1ae90 *NAMESPACE
7ca4befb5481a4c5fe73b9ecc2802ce4 *R/ExpressionAnalysis.R
bf13587bf8baa49d6a23b0625e5a589b *R/Graphics.R
5a95cc6f1b7c1377ba3068a6effeb234 *R/IdentificationAnalysis.R
a8b45cf25867c5ab6af490bc96c61f63 *R/Parser.R
605868730ed0304f1528a13c170b423f *R/SafeQuantAnalysis.R
9876f4ad821790c273de1203d732d3b4 *R/TMT.R
8e181920463752058bb15bb07d6259ca *R/Targeted.R
d55ad3c00e13c934dd8e03595f43ee06 *R/UserOptions.R
7a7648890bbf25f813f6a2fadddce77d *README.md
76a71967e16087c8bcb5bb204a04641c *exec/commitToTPPServer.sh
1c22b266aa80caed5796bcaa4ebc09ea *exec/createDocumentation.sh
213129760f9b98506bfa4901fc647ca8 *exec/filterLargeProgenesisPeptideFile.pl
f7f20f6c884d9df470e3932528bee1ab *exec/mFuzzClustering.R
2e46fd29fd20fecc9c955a04dad2f648 *exec/roxygenize.R
4df840cc1921ac1009f0d84b1fcd139a *exec/safeQuant.R
0bb5fadb5baacdc6f3bd14a8a9c04915 *inst/manuals/SafeQuant-man.pdf
1404e5d260a240e1b718e50aab5b06c8 *inst/manuals/SafeQuant_UseCases.txt
43b7ad06851418f2e168ae6d33fbeca6 *inst/manuals/tsv_spreadsheet_help.docx
8d8fab4f8d282066a9ca1fdb909aaed1 *inst/manuals/tsv_spreadsheet_help.pdf
3b4eee4b6e469967b4c8716f37dca679 *inst/version/TODO.txt
658119e29673ffafd63ee8236f17ef57 *inst/version/installDependencies.R
032b75062b42c3b8a6c85c54f0f2eef7 *man/COLORS.Rd
57d703273f1937279b3ed22e403f4105 *man/addIdQvalues.Rd
2f9ce3508dbc28f46c83ec7c20ad9c09 *man/addScaffoldPTMFAnnotations.Rd
328346b5e87bef108278454048be7839 *man/barplotMSSignal.Rd
08da127ad538a663c6c0763bd5f1d5b2 *man/calibrationCurve.Rd
a47212bdc214415d0f3c89cdda7c5fb6 *man/createExpDesign.Rd
4b8a278c85f6d7a7b3edc30ae2363be4 *man/createExpressionDataset.Rd
3300557a13e16418041ac5e506f5393b *man/cvBoxplot.Rd
a4147ce43b851562ed6f277821e409c2 *man/expDesignTagToExpDesign.Rd
78e7b9641525666c99d051783ef8f5b3 *man/export.Rd
2c76eb3eb6914a7072740fec16f45806 *man/getAAProteinCoordinates.Rd
3d236e108522af4b990248afe5981e5c *man/getAllCV.Rd
3bcbdb95a0fa5de5f3b278c8ace3a6da *man/getAllEBayes.Rd
d13bd126655d4df340652aa56f248ed7 *man/getBaselineIntensity.Rd
ce023d29048d7baead365534ec70f58e *man/getCV.Rd
e535c4c712b01e5e9bd5a0b88c1b4cdd *man/getExpDesignProgenesisCsv.Rd
3a9d0aa8f0ec4d5838434362251f32a3 *man/getGlobalNormFactors.Rd
4de191d9388192286ed8233a66a6f0ed *man/getIBAQEset.Rd
6ebf4a92b92358321f75206a85393459 *man/getIdLevelQvals.Rd
bfb560bfa32a4ed4be52eebb30be63e4 *man/getImpuritiesMatrix.Rd
87e81f8ecea995034516d9ff7d4f1f5f *man/getIntSumPerProtein.Rd
2d3cac1eee8147f0f10f755e3b1da4a9 *man/getLoocvFoldError.Rd
0a630c3e40f16fc0103c40ad4cd30213 *man/getMaxIndex.Rd
1d94e8d6a6aedcef77b0ca91ef5fc1c5 *man/getMeanCenteredRange.Rd
05b3244cd8827f4357b1662a135ff1b6 *man/getModifProteinCoordinates.Rd
3df43dd992b644a985f5d024539201b9 *man/getMotifX.Rd
ab09bf0602414b26e17c16f36840b8dd *man/getNbDetectablePeptides.Rd
34bc041abe1e057fa1703747efd82f4e *man/getNbMisCleavages.Rd
c264ea7e3793da31d37c9404740b7f49 *man/getNbPeptidesPerProtein.Rd
784a036e4c703ceed033db5bd951a737 *man/getNbSpectraPerProtein.Rd
d275a3d833bec99a43a133e452d865b5 *man/getPeptides.Rd
b85030a40833722131748acedf392dff *man/getRTNormFactors.Rd
af973a121d1026d713b651b3f71028ac *man/getRatios.Rd
b6e0afcac58a13e8fa13c7dfa282682b *man/getScoreCutOff.Rd
14d76534125857c927bad0628369b19f *man/getSignalPerCondition.Rd
fee0105475ce842d48b7442e5dbb5c8d *man/getTopX.Rd
3e749850636c76cd75353b03a1755d7e *man/getUserOptions.Rd
cc2b91ff9153cf3838492f8182067714 *man/globalNormalize.Rd
eadfc6855982f8e1ed3f0d28edcb4e00 *man/hClustHeatMap.Rd
52b2bca455e9c73c22c8e39f934cbb64 *man/isCon.Rd
c8f6dce3428b73ffdec116ddc83de589 *man/isDecoy.Rd
e4855f4b0a9c4236889076504b75703f *man/isStrippedACs.Rd
5d4229bd99fd883baf71d3d93dd95c8d *man/missinValueBarplot.Rd
cf0d0fad8013c032309da8fd9d238c63 *man/option_list.Rd
141848ca8411b8b6d0f1d68eab67551e *man/pairsAnnot.Rd
5765f7bd7333f7ea0b8bdb748fe50c8f *man/parseMaxQuantProteinGroupTxt.Rd
a28f8b7c3e62c771406d823245bc9c81 *man/parseProgenesisFeatureCsv.Rd
88fc47a6fc4b16ae8d0676567304301f *man/parseProgenesisPeptideMeasurementCsv.Rd
1329bd028a56ba9dd87e9f8065851982 *man/parseProgenesisProteinCsv.Rd
01a9619a2a9496f61a037c1ccf3773fa *man/parseScaffoldPTMReport.Rd
7594b20a5ad6cab14c9c6e410817808b *man/parseScaffoldRawFile.Rd
fec78d03eb55915c086d5c5a37947309 *man/perFeatureNormalization.Rd
d46d8e2afcef80d0c5902270db65b3d9 *man/plotAbsEstCalibrationCurve.Rd
44f84dcfc913cdeb3d3744685e97dd8d *man/plotExpDesign.Rd
1e8f4656fcb968fadddacef57ca90c17 *man/plotIdScoreVsFDR.Rd
05e5413819e0984450647cc64a6e9f1c *man/plotMSSignalDistributions.Rd
5afb4e33ceabdc66e6fbdc44c6702760 *man/plotNbIdentificationsVsRT.Rd
bba8bcf6651553724fbf9bd5a5fea5c5 *man/plotNbValidDeFeaturesPerFDR.Rd
2a17388e4783bd5f889758682c063c8c *man/plotPrecMassErrorDistrib.Rd
76483b675c7d67861115e16ccd56e6fb *man/plotPrecMassErrorVsScore.Rd
60da33dfb16626f4bfd19e643a05dd97 *man/plotQValueVsPValue.Rd
143c50cdbebe2bdf9fbffaa2f7ebba6f *man/plotROC.Rd
4ac349c0dbf03421e088526af02e9a3e *man/plotRTNorm.Rd
6f4cb545f688ba752a7fc7e0f980a051 *man/plotRTNormSummary.Rd
9165b2c5167c74ebd54947f1d19b05b5 *man/plotScoreDistrib.Rd
d9c4b2f2a95518d449c60b5e1a10b9b4 *man/plotVolcano.Rd
8c42ba58aca05bf138503566a063dfec *man/plotXYDensity.Rd
1548d5da643215fcb4df7ce7b3b1ef87 *man/purityCorrectTMT.Rd
d7bdbe7069dafe62b915299695ec6098 *man/removeOutliers.Rd
ff55d9f41be85d395b11ae7cdadbb5af *man/rollUp.Rd
d7fb161056c053f13e096412c3c9892a *man/rtNormalize.Rd
14828bc541b5c1b53f921d2c783af632 *man/safeQuantAnalysis.Rd
b7410b9cbeca1ca43af000721af12fe2 *man/setNbPeptidesPerProtein.Rd
82f3ec5aaafaee6b2f3a18e49e632554 *man/setNbSpectraPerProtein.Rd
8beb27043f0413d23c30d783c3e6aeac *man/sqNormalize.Rd
2cdc10aef2eb1fc939377e882f5d2897 *man/standardise.Rd
f7137d4e23ab7e90bf8bdaa1c65f63d7 *man/stripACs.Rd
cb83d31aa91ea5dc3580aeb320d376ef *tests/initTestSession.R
f7dd8697217a164c8a84f6e3bd2d7efd *tests/runAllTest.R
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
674e8d39d64ac48b7b91adec99724cda *tests/testData/scaffold_tmt10plex_raw.xls
c082dff4708ee54f3e86ad1f9ae540cd *tests/testData/scaffold_tmt10plex_raw_phospho.xls
43601181a3efe34f68d292e14c4afdf7 *tests/testData/scaffold_tmt6plex_raw.xls
6fa80d827bdef68757503408fa0934b0 *tests/testData/skyline_dilution_curve.csv
64d779ee274bb504f9fa805e1b73a7d7 *tests/testExpressionAnalysis.R
324eed6e9fec536cc051e48a979f7884 *tests/testGraphics.R
d767ee1d4c4260e63b4fc8bb50d6e127 *tests/testIdentificationAnalysis.R
44b0e5bcba79fee5734c21f6f94efbac *tests/testParser.R
32627dcc5f3d2c7b72116694dc4d5962 *tests/testSafeQuantAnalysis.R
ba4a8e6be33e9f8f5e9c1836a00e626d *tests/testTMT.R
9ea6e577c898bf2e2a0110ea3247a9c8 *tests/testTargeted.R
f130d7a9cb3bc7d3d0bd4abf7bd3b077 *tests/testUserOptions.R
