80eadc2b57a9c3b43c571e52880bb7c7 *DESCRIPTION
3704861b327db33fac1e44e391c9c1a2 *NAMESPACE
3bf06a4b95392491b8ba7947a2cd34ca *NEWS
f264fea3948f974c5971ee6a0e761e75 *R/JPP_update.R
825795869d84370c37ec4acab0a59dc1 *R/assess_decoy_rate.R
bd79d254116323e81cc582bc28481e93 *R/assess_fdr_byrun.R
49cf89908c2a52a68cf8d6d29799dec2 *R/assess_fdr_overall.R
63fe08ee2a32c89a958df5f6dcae66bf *R/convert4MSstats.R
0ccc224e984ab2332e482cf31fc48f9c *R/convert4PECA.R
5a4ac4f206ab0fa6398dcd156d65f08f *R/convert4aLFQ.R
139cc7f456b2214530669de0420d23b1 *R/convert4mapDIA.R
7eab60236c4ee64e8fe734ee786c3158 *R/convert4pythonscript.R
117e9d66b41362759b5698c228879492 *R/convert_protein_ids.R
afc11d75ab0c9237f504bb130d9fbcc1 *R/count_analytes.R
5f9b071b2f4d61bf87f1185894cb97d0 *R/data.R
088bde56662a6505c5b1f4c69591d5d4 *R/disaggregate.R
44f18f3ee4da2e5c564efda819af7c9d *R/filter_all_peptides.R
01ef0ed09e4bb5216596a171f0c699b2 *R/filter_mscore.R
de71568207ba05c77ff5ec84f63b7dc0 *R/filter_mscore_condition.R
93763c64a012ae131f440b8f4a0d3b22 *R/filter_mscore_fdr.R
cd51ca9abe8e75484b89eb33516986ea *R/filter_mscore_freqobs.R
0700ebb401dd968402c6896c4ca082cb *R/filter_on_max_peptides.R
d8072b93e3a804f9732bcf0e34ea60d9 *R/filter_on_min_peptides.R
f55d744a0a87d1e5ff1f4d41ad78b040 *R/filter_proteotypic_peptides.R
d0fc203f4f137f675958214c281ca54d *R/import_data.R
5e737ee0569ffc2da68a759c0b1f3bfe *R/mscore4assayfdr.R
5aa3fc15810ebecf28f815fc12ce8f33 *R/mscore4pepfdr.R
f5cbf5ededa91b87c685cab76159c508 *R/mscore4protfdr.R
b613e8203d73dc0f56c0ee4e898c045a *R/plot.fdr_cube.R
e36e7fb06878b2a99aeadea59f3e4a89 *R/plot.fdr_table.R
85e5873ee777243c99ea5a7122450202 *R/plot_correlation_between_samples.R
b0f9f05a648fa57c91a70d499f3fe753 *R/plot_variation.R
40e713d29de28d0408060b8ae07ab4e4 *R/plot_variation_vs_total.R
5703dd9ee6c2e105df2112d75d5ce8ab *R/reduce_OpenSWATH_output.R
2b5c9100b1aa249857c5ef9d3d3c8b2a *R/removeDecoyProteins.R
7fc15d51230e5add589b81071593d7f5 *R/sample_annotation.R
539779acc8f19f3cb485201822939a24 *R/transform_MSstats_OpenSWATH.R
720a07ed593dd08c556cc59fd79abee5 *R/unifyProteinGroupLabels.R
491e10d0488339dc8cf4788ec744c1fd *R/validate_columns.R
d8930841fa7a949943f67c22804482ef *R/write_matrix_peptides.R
456038f1f26e7165b06fe7dcbf039f3c *R/write_matrix_proteins.R
b7ffc5879d5b81c246a2836930dfc8c9 *README.Rmd
2fecab8086b256ec6bf47a0c73f96244 *README.md
8bcc1f2c7e878680d8659f5fe80263e8 *build/vignette.rds
d8a04082bc5dd10621c29f5be1883e98 *data/MSstats_data.txt.gz
805b4978ecdcc0c525ff7ba1ff7b1097 *data/OpenSWATH_data.txt.gz
5567f04147091eb68cf9812cc29aa400 *data/Spyogenes.rda
0aea942e52d15d55a4352bb843015d02 *data/Study_design.txt.gz
5779495d17b209ddc8f62b0e056bb20e *data/datalist
b8cccee4efe2ae91457eb46ec5594cf3 *inst/CITATION
6c09f11ca41790db65fd32a9027a59d0 *inst/doc/SWATH2stats_example_script.R
781b231ebfc31259034dfe826f80ff31 *inst/doc/SWATH2stats_example_script.Rmd
016beb08323f1ea6eb37f046be6028b8 *inst/doc/SWATH2stats_example_script.pdf
c81a544db4b3472d737efc7793322ca4 *inst/doc/SWATH2stats_vignette.R
297243d9e29cca3eff822bfb8e0921eb *inst/doc/SWATH2stats_vignette.Rnw
416919f609b5e89002c0fa997b6a1c35 *inst/doc/SWATH2stats_vignette.pdf
4a17d53a9c897f818bb0bb30523d0449 *inst/scripts/featurealigner2msstats_withRT.py
ae91630545812639d832ff1e4067c7a0 *man/JPP_update.Rd
2a872af9050a32ca29c53f345c3bb17c *man/MSstats_data.Rd
d65f375472c0dcc0e853138a07e69d00 *man/OpenSWATH_data.Rd
d8274bb1fcf11947ea80e6f77968be86 *man/Spyogenes.Rd
e7a41d6c1fe6be7e3c83cc6f763b79cc *man/Study_design.Rd
c267cea8609bc29305b210539b162727 *man/add_genesymbol.Rd
bd65da9e7a078dabdfbc8db6f2b6ecce *man/assess_decoy_rate.Rd
19af81a7ba750daee8e5cca6a6b79788 *man/assess_fdr_byrun.Rd
09cdcc21b7d2977ddf399cdd6081cd5e *man/assess_fdr_overall.Rd
261e220853509a4cda28e0d1cb396c2e *man/convert4MSstats.Rd
d6f2f6d7746761c25decf197d759cb75 *man/convert4PECA.Rd
9e7258eb0126d5c8402f545950918fb0 *man/convert4aLFQ.Rd
80e1eeb6bf814bac74b941ea78236ecb *man/convert4mapDIA.Rd
557dfbcbf960998b86990ec1d26a4085 *man/convert4pythonscript.Rd
45860c0dc5e7dcad566c792c28188517 *man/convert_protein_ids.Rd
3f17b76f4be592636b0fa749d8bb38b8 *man/count_analytes.Rd
6725ac33b51a716c25b913712fa5963d *man/disaggregate.Rd
ce42102ce46bd61748416200c23f42cf *man/filter_all_peptides.Rd
c825930a254086e1a1dcfad0dc9ec213 *man/filter_mscore.Rd
7062243dcddea539c88bc96075e8964b *man/filter_mscore_condition.Rd
9e3c508e612767525e445989372cf321 *man/filter_mscore_fdr.Rd
23921627c2bb61dd7409a811eeccfbd0 *man/filter_mscore_freqobs.Rd
60c8f85a6840052a0a6213f64de0ade1 *man/filter_on_max_peptides.Rd
3f34dd4212792004d57d1bb780004deb *man/filter_on_min_peptides.Rd
4ff724b80e0f4cca0edb9700f74aba85 *man/filter_proteotypic_peptides.Rd
a380e0e419d6821170c85f0fd501ad6e *man/import_data.Rd
1cee64acfed9ad740348337766083b26 *man/load_mart.Rd
2fdc56445caab2de398c8a8dec13c86f *man/mscore4assayfdr.Rd
3bae0856259acf9b23045dc956547a25 *man/mscore4pepfdr.Rd
7945eb7cb0262b0e3583f765250ac444 *man/mscore4protfdr.Rd
1fe81dca2fb05f726d3ff60701a1b0c9 *man/plot.fdr_cube.Rd
131f6660cac3c7078d20edc4bc9c23e0 *man/plot.fdr_table.Rd
a39c6b9fad03b18ada9cb7ceda4c84ee *man/plot_correlation_between_samples.Rd
d217cb7b2f6d35c8ca2472fc1d9104cd *man/plot_variation.Rd
d11dd4fb3881ce340023261ddab78f1a *man/plot_variation_vs_total.Rd
851f167991791197378ebfbb266c47cb *man/reduce_OpenSWATH_output.Rd
0ac21ca357ac8808d7ff5b289526a822 *man/removeDecoyProteins.Rd
7852e1938c2bb3613daac401caefb9cd *man/rmDecoyProt.Rd
e05a83dd56f42c806c3d239748916a00 *man/sample_annotation.Rd
7c30fbb38812630c138539202379f1aa *man/transform_MSstats_OpenSWATH.Rd
cbed2269b5caf8e3f33f0ffd8f28ac4f *man/unifyProteinGroupLabels.Rd
efaf8911f9549279adcf612403ff318c *man/validate_columns.Rd
8c9cf7da0afb795f85fada435ada2f33 *man/write_matrix_peptides.Rd
b7aa4110e74c921c3f2059e6f6cde048 *man/write_matrix_proteins.Rd
28b59870aa95deb6d68668a0f1eb8ab7 *tests/test-all.R
d16dd5fbe71d957b23d4cfb792d44988 *tests/testthat/test_FDRfunctions.R
4a121610febd18db4505fc62ee71a15c *tests/testthat/test_biomart.R
8d7a17a6e7385887228ed6f385f94a81 *tests/testthat/test_convert.R
11a2ffa4d3dd4c1c4d47554d39b2acdb *tests/testthat/test_filtering.R
3884aae97802213ca0e9044dae7febdf *tests/testthat/test_loading.R
249f1282f1dce4c924edd7d0aaa3e399 *tests/testthat/test_matrixwriting.R
389e1289c1861bc2b4f64c2fc6e62ae3 *tests/testthat/test_plots.R
781b231ebfc31259034dfe826f80ff31 *vignettes/SWATH2stats_example_script.Rmd
297243d9e29cca3eff822bfb8e0921eb *vignettes/SWATH2stats_vignette.Rnw
