50525717a730d0c4fa525d5d73ead9b5 *DESCRIPTION
13164d11c5767f2e9b3208e54081984b *NAMESPACE
bae472b692fdadd049cce8dd3b4108ea *R/basic_visualizations.R
a8d11351a27c58e848922eb3c99c27b2 *R/dataImport.R
185fbf5f9bfc8b1df7adfbc31ecafb2e *R/dataset.R
11a94cddcb4d4d2f0fbf2c0779fb6bbc *R/differential_expression.R
6246706a8d01f2586e81910694feb3d7 *R/enrichment.R
a8f9b11bbb04f3797168a4fbd3bf9f84 *R/helper.R
3890b648f2f61ed76bcc25ef8905ccde *R/kinase_activity.R
a2ed868166c2feebe273ac54d0ad5b83 *R/normalization_correction.R
5f4b9af0b93a4871453256dd415b4881 *R/preprocess_proteome_phospho.R
5fec3b43533be8648aa695be47a60284 *R/shinyApp.R
b3f8fa5bf6b6375b75f55c1954ee3dbd *R/time_series_clustering.R
a1d9e65bf23f124d5a5c5be7411875dc *README.md
61ae5ea3fe38331c4cff15e3005239ec *build/vignette.rds
bd1a0810eb5dc494bacf285a26cdc2b1 *data/Homo_sapien_kinase_substrate_network.rda
dc9d8be0657fefc2fa8c92a8362acffb *data/Mus_musculus_kinase_substrate_network.rda
f157a310767f73c4f4ef2ce6c28c80d8 *data/datalist
65d3517d81c2349575dd1128a7e0c64a *data/dda_example.rda
d2274385eb30c0ef47554f3b7c5e1686 *data/dia_example.rda
8356e2a21df92d291548452005e83d18 *data/swissProt.rda
d906ab5e5130ec0c224cd729fadb4990 *inst/NEWS
bda1c464aec398ee9c6754bd5b71a636 *inst/doc/SmartPhos.R
bfdf1079eac0b84a2077ad7ef445d99b *inst/doc/SmartPhos.Rmd
edbd3ae8bd16444fc84dfdb06417c372 *inst/doc/SmartPhos.html
38b11b8b871c9dbf3c695bf6c6733e32 *inst/doc/SmartPhos_Shiny.R
d6a9d5a8f64260c49220179f5e98077b *inst/doc/SmartPhos_Shiny.Rmd
0f70a0b4dee97ed0cb107d85711b8d51 *inst/doc/SmartPhos_Shiny.html
dc56317f37f68453a982de6eab7eb4a6 *inst/extdata/phosDDA_1.xls
49119c8d26c997c1e3478c624512d0a6 *inst/extdata/phosDIA_1.xls
bb6562bd5f8497149fe62b12a4c75705 *inst/extdata/phosDIA_2.xls
3aa27f6ff18e57f335b05371d3da07b4 *inst/extdata/proteomeDDA_1.xls
f083890c271770bfc2f05c58d53b8326 *inst/extdata/proteomeDIA_1.xls
dcf0b8302a7babba6fb0b1e0580b4416 *inst/extdata/proteomeDIA_2.xls
68cb4ea844fa3ce7ed9b0fe99f24420a *inst/scripts/extdata_generation.txt
04bdb4176df51a0730186a8784a733bb *inst/shiny-app/geneset/Cancer_Hallmark.gmt
a7d3895c31f15d1d61d511ab7ecb663c *inst/shiny-app/geneset/Chemical_and_Genetic_Perturbations.gmt
9d9d492a3f374b888819235f4801afa4 *inst/shiny-app/geneset/GO_Biological_Processes.gmt
5445b9420795d4238a9e166cde3133a8 *inst/shiny-app/geneset/KEGG_pathways.gmt
e10c7313a4977ab1016ee89dca648b14 *inst/shiny-app/geneset/Oncogenic_signatures.gmt
e1198a4b675fdf729a68fc841dc2e889 *inst/shiny-app/geneset/Transcription_factors.gmt
1e3abccadaf993fdb910ba1c8fdb997d *inst/shiny-app/infoTable.tsv
a1d2e6d94afd4742af002444abe44fd2 *inst/shiny-app/ptmset/human_PTM.rda
a6aab12cc1c21395ba4731125a1d5226 *inst/shiny-app/server.R
7c837007162ac07bfc8f96d063269598 *inst/shiny-app/ui.R
79152bba646e88584919825dd07a5165 *man/Homo_sapien_kinase_substrate_network.Rd
2858571a7157e3165c3ccce1d766981d *man/Mus_musculus_kinase_substrate_network.Rd
4e09b90025f07cc991c4c4c3f6cdb042 *man/addZeroTime.Rd
d2342e9a53585b2469a03687f192d1ce *man/calcKinaseScore.Rd
e7c6b60d1c42b1861cd64640e608df7e *man/checkRatioMat.Rd
e7380e656be4d38366f944d2ca2dadab *man/clusterEnrich.Rd
65f5d405e63b4b334ea72264e4e90fd7 *man/clusterTS.Rd
8ff33ae2b33deb7b187fac1692f03672 *man/dda_example.Rd
a4c5ffc8276a960545a552bc42e75b12 *man/dia_example.Rd
b392156e406d4c8e3d1c6cbae9bdedde *man/enrichDifferential.Rd
d96968099acf02920f86d24ddddcbfe9 *man/generateInputTable.Rd
03152ce508e1df5bda35fb2738d420a6 *man/generateInputTable_DIA.Rd
2efdc603f6884307c5cbed9b2ecb3703 *man/getDecouplerNetwork.Rd
136a6397087cadc0d09a452288226c31 *man/getOneSymbol.Rd
1f47c6fcfdb03e6e894887471384799c *man/getRatioMatrix.Rd
1077a214d8763d81479e40ccf03936b0 *man/intensityBoxPlot.Rd
b38a8d39accef6feeb29d99537868de0 *man/makeSmartPhosDirectory.Rd
4b67e906ed17928f2327ab293a1eec33 *man/medianNorm.Rd
f08a3677bb51e4cbcb11eb3f5d4bf16d *man/mscale.Rd
0639e6b34653daee55cbed8e37e80549 *man/normByFullProteome.Rd
0caf03a74a7190ec9592a5b8e518fbcd *man/performCombinedNormalization.Rd
052ed52cca3a1847d06f7d074a67b22b *man/performDifferentialExp.Rd
e5a19470d284faf94d57adebcb9ec88f *man/plotAdjustmentResults.Rd
904af76de86489f95256e3aa102f20c1 *man/plotHeatmap.Rd
07edde58c263ff0fad246ee95ee09d63 *man/plotIntensity.Rd
6cab02aabaca0f3a5472f33eb3424711 *man/plotKinaseDE.Rd
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5ee73f041182696eda20a6a97e9f93fd *man/plotLogRatio.Rd
24319cb877b92fc03ccef3fcb8f8a442 *man/plotMissing.Rd
feec0d490310c99528c728e912ba306a *man/plotPCA.Rd
730dbabe223499f2db6bc2973fe37581 *man/plotTimeSeries.Rd
a34c2fa63eb1d9ec3b5e8313600d84ff *man/plotVolcano.Rd
f73bd1ee218a3715f70b688223c8171e *man/preprocessPhos.Rd
dfc45b682b2725795deea238258bb69d *man/preprocessProteome.Rd
c338c0f48a4e13d86a18fe876ff4cdbd *man/readExperiment.Rd
395913f9c79dd93921d8f3ef7d99b85d *man/readExperimentDIA.Rd
498767fd599c509e8f105ffb4f149cab *man/readOnePhos.Rd
e072770074f82b5bb4565279f9c60351 *man/readOnePhosDIA.Rd
91616b43803ea93e85758f7b052ba242 *man/readOneProteom.Rd
fc8d8f38cea15dd7854f541ae7e0ed44 *man/readOneProteomDIA.Rd
bdc358381072ddd111f8a036b6f84587 *man/readPhosphoExperiment.Rd
c5595bd7f6bcd6c7e6d6a33fa98fca90 *man/readPhosphoExperimentDIA.Rd
acbe3dca627490d14af5e4dfbcbe0f8c *man/readProteomeExperiment.Rd
48606ef49f42719736040aec2721393d *man/readProteomeExperimentDIA.Rd
9444b11294677eb0b8ae36e150a39e1d *man/runFisher.Rd
5d49bfbbfbf49145f4c221d41831e0b2 *man/runGSEAforPhospho.Rd
7603bd23e469d9d9860394747ad791d7 *man/runPhosphoAdjustment.Rd
162d75f04be522f2aa9d6ef39dd45c8d *man/runSmartPhos.Rd
ac7b76213c48fb7f4a8ab21eaadac6f6 *man/splineFilter.Rd
a38b9e3ab47c213f2a3e582a10b09627 *man/swissProt.Rd
a4bd2bc796d5ffa771fd66d7a412f19c *tests/testthat.R
7669b62a2c686809b79d87d2f241404d *tests/testthat/test-basic_visualizations.R
0760c1b3d6453302190cef1d4fd9bbdd *tests/testthat/test-dataImport.R
f55b0f675dc900538d01c282af30b8f2 *tests/testthat/test-differential_expression.R
143588b7c76eae62a386a8f8444bd101 *tests/testthat/test-enrichment.R
281adea2c5371f5bfa0b101dda6f18d6 *tests/testthat/test-helper.R
77e33582dadcbd1b8ec6518d3aed1093 *tests/testthat/test-kinase_activity.R
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eb60f5aecfe4041cb19c8bd7cecdee9b *tests/testthat/test-preprocess_proteome_phospho.R
398d15f048f2a0dafad6c3840af18251 *tests/testthat/test-time_series_clustering.R
bfdf1079eac0b84a2077ad7ef445d99b *vignettes/SmartPhos.Rmd
d6a9d5a8f64260c49220179f5e98077b *vignettes/SmartPhos_Shiny.Rmd
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