335f2a197cd1fee9510f06514ea8f91f *DESCRIPTION
86cd0b6e13d5c2d93423f5cb59f7d0c7 *NAMESPACE
b97ac610388173d94a1ca3f5c717e675 *R/MSstatsPTM.R
5d614044d167ee5b564c7edb3805a1bc *R/RcppExports.R
3b781c5696bdeeda6bf1d2d49bfcd640 *R/converters.R
0bdb2302327f98d26db4e319c8e66683 *R/dataDoc.R
24e9b69f96a28768e0115ceb71e77d75 *R/dataProcessPTM.R
47122572515e9e6d97c63d414bbc3dc3 *R/dataProcessPlotsPTM.R
ebb4b3f5e9ea97f91740eaa673156b5c *R/dataSummarizationPTM.R
1a094ef683b28f203b05a4a39c6c58f4 *R/dataSummarizationPTM_TMT.R
ca57ca20bbc36bc51a7a95e8c7571227 *R/designSampleSizePTM.R
8e5fde753a962f8e00e24b49a42b75f7 *R/groupComparisonPTM.R
60280c0552aae49c0c70eec8a9a4bce5 *R/groupComparisonPlotsPTM.R
99f9e77dbb08fb5f628be3919c15756b *R/locatePTM.R
7a4fdffba3d8a033e5c8e67329eb9157 *R/msstatsptm-package.R
6daab8526433a16a6724c392980067b0 *R/utils_checks.R
a5a495e94ae96981a4702a3bb328af95 *R/utils_converters.R
d7a7e52d705042bd735fe9354ef96ddc *R/utils_dataProcessPlots.R
da4f247e575051d47b9a5b408dbc2569 *R/utils_groupComparison.R
54dba3c1caf0f83e732a06b2ad3532cb *R/utils_groupComparisonPlots.R
b9e87dc4f7c037e2258c1688a69d86c8 *README.md
0fa315faa4414d24579998d1082798f7 *build/vignette.rds
8a29d3ac0ab7c34bf4a3c4382e000241 *data/fragpipe_annotation.rda
a76c6cbcac9b692f57b8a51adb9fe3a3 *data/fragpipe_annotation_protein.rda
524b94271af1c0e03aa299e73cb6ff93 *data/fragpipe_input.rda
b346cea6edd5316357340f20659b4cb5 *data/fragpipe_input_protein.rda
e4540e42e89786062ca0e3642accd66a *data/maxq_lf_annotation.rda
86c8a8b731507066d7067832a14b51e3 *data/maxq_lf_evidence.rda
094063e4f28301fba0aba536b50787e4 *data/maxq_tmt_annotation.rda
31bb7d12876c5a0004bd1375395671b2 *data/maxq_tmt_evidence.rda
4e50ca1501b26dce2bcc0d0cd7ca145b *data/pd_annotation.rda
0cdf4511c31fb999d26f3830fdccf3aa *data/pd_psm_input.rda
e32164ccf938d02504a879914d18494b *data/pd_testing_output.rda
fd12405a34ec0f327219a68275d4d269 *data/raw.input.rda
68a18a86dfce4b01283070218fc7bd36 *data/raw.input.tmt.rda
d309901fe82636e6e2954235e3bf6788 *data/spectronaut_annotation.rda
e0c403c18498709e607cf5b535364d69 *data/spectronaut_input.rda
a4ed4ac89d084f34f636d2faea779922 *data/summary.data.rda
d41451dde63ee0d66125cefc1045bf1d *data/summary.data.tmt.rda
82dd64a02a131a6fbe14b7ee60db6fb9 *inst/CITATION
f32d7b1cf13bcc0e0986678db02fc166 *inst/NEWS.rd
7a75500122333f6e8d83533875097a9f *inst/doc/MSstatsPTM_LabelFree_Workflow.R
c8ada2c76df5317702b00a58ae1f3941 *inst/doc/MSstatsPTM_LabelFree_Workflow.Rmd
96786a98983dfacd9f6c18cd98c01846 *inst/doc/MSstatsPTM_LabelFree_Workflow.html
4c0367ba54ea52826116f7a4c1b324e3 *inst/doc/MSstatsPTM_TMT_Workflow.R
5aae19c87ee7c6b2e6224841b684c59b *inst/doc/MSstatsPTM_TMT_Workflow.Rmd
45c51e4ce715ea483d242bedfb793a5c *inst/doc/MSstatsPTM_TMT_Workflow.html
ef9d05deedb9b779c780712c81e19eba *inst/extdata/O13297.fasta
bf319d8bcce43f2f6f8d8574747bc271 *inst/extdata/diann.fasta
03a627bbe7678e8470693d7a482ed8ac *inst/extdata/maxq_lf_fasta.fasta
e0b43db2fe12100747a3b7ce079543e8 *inst/extdata/maxq_tmt_fasta.fasta
1846d9ecb1c8c9b160dc6a11da78dd8e *inst/extdata/metamorpheus_fasta.fasta
d076e1b47eb4230a0fbcbe6e309a3ab2 *inst/extdata/pd_fasta.fasta
1ee93cb9a7ad1a6e2b4ac88fa0179f4b *inst/extdata/pd_with_proteome.fasta
f990f48387c98b9842f72fa8768c1326 *inst/extdata/spectronaut_fasta.fasta
f036040745ab4ca3810f060599ae3bb1 *inst/tinytest/raw_data/DIANN/annot.csv
fc498f940fcc0b7e5af41d7c56bb5d1f *inst/tinytest/raw_data/DIANN/report.tsv
687bdf011108bf5d7a9dea1f24cd5dba *inst/tinytest/raw_data/Fragpipe/MSstats.csv
86386dc3c7fb9823968919a01f5407bc *inst/tinytest/raw_data/Fragpipe/experiment_annotation.tsv
e19f0a7fc776e643add3bb9bfac76d20 *inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv
d71d8136a58413b67a8ae42dc04362e8 *inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv
39cb0ead7dba8f5fe3ba927afdbecf0b *inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv
630ed4124f8d5f3c0d350cbd45305797 *inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv
06f3d7ebd519175d838867cb218ca509 *inst/tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv
93475a25005eb82e3b8a169cf4fc2a37 *inst/tinytest/raw_data/PD/pd-ptm-annot.csv
24bd96285718ddbbd9c45da82c08d93e *inst/tinytest/raw_data/PD/pd-ptm-input.csv
a75f7a58efa8057549e10c9030390d5e *inst/tinytest/raw_data/PD/protein-annot.csv
a12b262ad649f437801a848d4de27cb3 *inst/tinytest/raw_data/PD/protein-input.csv
72dbecb8583a31b038f69e5e5e9ca387 *inst/tinytest/raw_data/Progenesis/phospho_annotation.csv
d51294f6d14daa6850e44f2d5508e3a4 *inst/tinytest/raw_data/Progenesis/progenesis_peptide.csv
62b318642fa249fad6d1acabd2adc65d *inst/tinytest/raw_data/ProteinProspector/Annotation.csv
ac4681835dd87871c2f136f5e33ae40c *inst/tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt
b8c1678489e7fa6c86d8dd181a65300d *inst/tinytest/test_converters.R
e9655fb8a33d0583f47254404f2f5878 *inst/tinytest/test_dataSummarizationPTM.R
7512662de5a1c4c5a69c5ca7e790b335 *inst/tinytest/test_dataSummarizationPTM_TMT.R
3f56b0f201739f3cdb0136c73a5bd361 *inst/tinytest/test_groupComparisonPTM.R
341694541c1f402ac83bbedf81e0fbb1 *inst/tinytest/test_utils_checks.R
ab8a9a8dca4a75d6a45c81057b7d5cc2 *man/DIANNtoMSstatsPTMFormat.Rd
f827e4cc87581f0aa71d37b7e0ca8943 *man/FragPipetoMSstatsPTMFormat.Rd
3d75d9dbaf8a51efcec4bb8c7f951223 *man/MSstatsPTM.Rd
41f89563b9de408c0c61743af9bf5e66 *man/MSstatsPTMSiteLocator.Rd
22687fb8023395bc7802c044a6e64792 *man/MaxQtoMSstatsPTMFormat.Rd
48bf942f3ed0a76ce208c2a195032fa8 *man/MetamorpheusToMSstatsPTMFormat.Rd
37d4b99e8d5b9bd4ed22b95c912c91e6 *man/PDtoMSstatsPTMFormat.Rd
84e07023f6e933ba4524243db2a5a4f5 *man/PStoMSstatsPTMFormat.Rd
abb6aace51b3659e95d31a95523e973a *man/ProgenesistoMSstatsPTMFormat.Rd
257740d961c555f7673cb926cba911de *man/ProteinProspectortoMSstatsPTMFormat.Rd
b503956691ed12f94abcc94fdee65a0f *man/SkylinetoMSstatsPTMFormat.Rd
25be20cb6692c41b03b0f72c81e978f8 *man/SpectronauttoMSstatsPTMFormat.Rd
ee26a7019cfbf627e64f924d8391c394 *man/annotSite.Rd
540b72a89bf315b44bf8ead103acb631 *man/dataProcessPTM.Rd
fd07486b3ae99d39449bb494e7c65799 *man/dataProcessPlotsPTM.Rd
f28edc35a3f2a11e0ecd08bff0f346bb *man/dataSummarizationPTM.Rd
4b96177f81b643d032f60c19dd97ef45 *man/dataSummarizationPTM_TMT.Rd
449789b6fc83c9c5854f18929978550f *man/designSampleSizePTM.Rd
6cb0948b06f286f9180df69fdefb23e7 *man/dot-calculatePowerPTM.Rd
7ed8c7598868f04f0fd1a8235e91cfbd *man/dot-fixTerminus.Rd
4849aa5cf97c9fea9cd3b5c2f2f1f919 *man/dot-getNumSamplePTM.Rd
29607b0b5e8761a6af536fa296393511 *man/dot-joinFasta.Rd
3614f478ff006d06b15b784935f577d6 *man/dot-locateSites.Rd
dfdd6a99bf4e84a73d48c6294c252bed *man/dot-removeCutoffSites.Rd
6b2370414ac8220a64b13be410cc95fe *man/fragpipe_annotation.Rd
bf481ddd6cb78222bb39edb17544c3c9 *man/fragpipe_annotation_protein.Rd
eda98867e46bcb533a737f1275c24e13 *man/fragpipe_input.Rd
9e62090defbfb9811a72bd63b5a70d2a *man/fragpipe_input_protein.Rd
a81751d38a2ac2d673a1b24ac6cc04a3 *man/groupComparisonPTM.Rd
3e356823472b9c57454004b4074fa7e1 *man/groupComparisonPlotsPTM.Rd
b86ecf1917987bdeed5f870064c88d08 *man/locateMod.Rd
6d7c64e3fd3634fe27d3e1e023311f51 *man/locatePTM.Rd
8f63aee700bca515531025fb8601a8eb *man/maxq_lf_annotation.Rd
11cb29b523c174580b8b1d3499ab0215 *man/maxq_lf_evidence.Rd
20febcb696cc6fcb835c2f79b045d335 *man/maxq_tmt_annotation.Rd
8db9739c09e18049e3a09ecc13db6b7e *man/maxq_tmt_evidence.Rd
22737beb154792a85812b34be865b583 *man/pd_annotation.Rd
b8878e110a4925f8410a31e295e971ab *man/pd_psm_input.Rd
583a7dc74bbed95d3ce2c1708ca4652c *man/pd_testing_output.Rd
19655d24deb6cacb9834efea02a14270 *man/raw.input.Rd
f4b8d4973aff32dc29c8698403a4662b *man/raw.input.tmt.Rd
9da9e927b870f21542515086dc237a50 *man/spectronaut_annotation.Rd
1b587f7524835f3cd821832c90f1f91b *man/spectronaut_input.Rd
0dad9ad389803a27c3d070bdbf81c755 *man/summary.data.Rd
3d1991e141744e6eb24b0ff4f5d8121e *man/summary.data.tmt.Rd
ac9238018dd27d5260d268c8d03fb4ce *man/tidyFasta.Rd
da59451399130922f4973040892f8112 *src/RcppExports.cpp
aa860fb1af1c8f58ab674c5db0f31064 *src/model_adjustment.cpp
5dae670f7b7167583f265bc85e076c7d *tests/tinytest.R
c8ada2c76df5317702b00a58ae1f3941 *vignettes/MSstatsPTM_LabelFree_Workflow.Rmd
5aae19c87ee7c6b2e6224841b684c59b *vignettes/MSstatsPTM_TMT_Workflow.Rmd
