53b3d1d264bac07a3430c9e6da69c94f *DESCRIPTION
eb916b5824cc0592d993e2a15fc4d71d *NAMESPACE
8f18816df50abdc018587e87817f0c99 *NEWS.md
a69ca066fa9cf6240c84e8b9c44411b6 *R/BH_diagnostics.R
36540e8cff04e772621d06be102ea6b0 *R/BH_elasticity.R
4912108359473121d8193475d1364106 *R/alert_basis.R
1cfc03b3405049e63bd6872857040866 *R/class_dfdr_tbl.R
569c0b3022f25149b217dc9f31d20e4c *R/dfdr_summary_headline.R
90386f70fd28085ea79ef86475fc03ba *R/diag_calibration.R
8b7a776aafb292512ab3dedc61f7827e *R/diag_p_calibration.R
e30b6b7c3fb5e38c51b607778b900640 *R/diag_scope.R
6cd63b6f1636b25c11ac14f051d19d23 *R/diag_stability.R
ade3de7d69160b1c835b6cedac2dc544 *R/flag_headline.R
5553814bbbaaab44a3505c2925374aee *R/interpretation.R
17dfd35a1568834711aa6d3b79a77e75 *R/io_diann.R
688e9b3bb4a69a4d18700c4fb10e66ab *R/io_mokapot.R
8fd625bbc541f330258ca8cc00b0d814 *R/pi0_storey.R
9f8cd72ec4c9c5d83d9a3ad6dbc4007b *R/plots.R
09c4a7d84ed4f24e25b90e5c212463ef *R/pvalue_helpers.R
c9f1d311afbaaa0471268deb631db6c0 *R/read_maxquant_msms.R
b3ffceb46869c04a0f5b5d653700dd06 *R/read_mzid.R
156d53dced2d9de6a636bfd1797fbb9c *R/read_spectronaut_normalEG.R
2029f490c0621b626de214780cdacfd2 *R/render_report.R
61ba61cf5a7e411650e764c52f220fdf *R/report_write.R
35d884f5e6d0a79d0f738a88b9d63887 *R/run_all.R
557b4ff0c71a67c4b31b175d932ebc1e *R/score_to_pvalue.R
657b66054c1a05047ffec2e10c1f93b5 *R/utils.R
a4a6a59f7892fe27fa5fccca40a05e83 *R/write_manifest.R
5fabd5a44f11bc3d88936f146490d726 *R/write_readme.R
f30f83cf61aeba186ab9ac3b7987db0a *R/write_report.R
064c1141c19902ed44fa567fa608c26f *R/zzz.R
d1bbee67f72722c1e1aa6ccf92a48cdf *build/vignette.rds
42bad37237e5bb7282f3a3f0957a9974 *inst/doc/diann.R
be779263b81277793026791caa6aa17d *inst/doc/diann.Rmd
4009f70c4dfcce62298a420e0837c62b *inst/doc/diann.html
0c122545b82acb6d90b5aa93d9aea9ee *inst/doc/maxquant.R
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439f569164e512eb7b27ac7deb281f8b *inst/doc/maxquant.html
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2197e55e421b06f0efb7e33474680630 *inst/doc/mokapot.Rmd
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0e73f36f650b6e51f9a19c439bb406af *inst/doc/mzid.R
f6a85d0407e176f1b72f250e86a9d3c3 *inst/doc/mzid.Rmd
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0f7fd095000e99905e801285cd48d645 *inst/doc/spectronaut.R
a016737fd522f2b4358fec3a9c06bdf2 *inst/doc/spectronaut.Rmd
6dd8e9d110ca3fa4e901083cdd5bd8df *inst/doc/spectronaut.html
53081e2d8cf09095585f54b15df85d99 *inst/templates/dfdr_report.Rmd
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ab3b1fc6c5968be29bdefd7bf9a29f9e *man/as_dfdr_tbl.Rd
6f699a7da9c364350572222724a35630 *man/choose_low_conf.Rd
5c4ce63fe97aae42d34b3a6534da1ee8 *man/compete_max_score.Rd
7589b3d716dcad77c71c1f72613e3825 *man/dfdr_alert_basis.Rd
efb5b74a3c2f9f059adb48f65c019ca5 *man/dfdr_bh_diagnostics.Rd
91ad5aa0aa047dd8bc5f28445662db4b *man/dfdr_bh_elasticity.Rd
9a6b6cc9f30ecaf118cf1cf709f5ee0c *man/dfdr_curve_stability.Rd
9153fa4f44a579d56ad7649f0ba43980 *man/dfdr_elasticity.Rd
6fe4afb74a462ed7d77798492861a22d *man/dfdr_equal_chance_qbands.Rd
1a874e828e6410056f23e2fdf9ec517b *man/dfdr_headline.Rd
f3d2441f3432af6c9ce5c3e532f33606 *man/dfdr_ipe.Rd
56d17737c77e6b1aca34108d871fe6b7 *man/dfdr_local_tail.Rd
3c969ce8db3d6ce39b07d16adf79405e *man/dfdr_p_calibration.Rd
8d2c6e27811da50a8baf65ff782737e7 *man/dfdr_p_interpretation.Rd
f099c8cdb9b8e4c5f571bab405488dc4 *man/dfdr_p_summary.Rd
2be8a8c50a8b17c474581f6b50ed0733 *man/dfdr_pep_decoy_sanity.Rd
413552cc4a97182c2a50571f483ef073 *man/dfdr_pep_interpretation.Rd
433e06120805072a95c31a1b51dc731c *man/dfdr_pep_reliability.Rd
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26479bf055fbbe512bc701e361cfc52d *man/dfdr_pep_summary.Rd
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5cbc9a5becc9b5b84e990c5f1fc1cbb5 *man/dfdr_plot_bh_elasticity.Rd
7ab7c4032d238ebd2d3d42f9e7a3e802 *man/dfdr_plot_cv.Rd
7afa2c9a8a183d2c6b5df943df88fb56 *man/dfdr_plot_dalpha.Rd
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be07ac24d168be721726192d0cee9783 *man/dfdr_plot_p_calibration.Rd
a484ccf53d7923abb8460cf327ad9f44 *man/dfdr_plot_p_calibration2.Rd
0f3f23abe93339cd3c3aba8bc960a5d9 *man/dfdr_plot_p_density_by_decoy.Rd
8e0146f27eaf33edeba49579410550c3 *man/dfdr_plot_pep_density_by_decoy.Rd
d43480f15fc467534d10f1231c904bf6 *man/dfdr_plot_pep_reliability.Rd
355e8b814085b31955327eea44e223fd *man/dfdr_plot_pep_reliability_tdc.Rd
b57b570d89c4524275b620cec0ed5fe6 *man/dfdr_plot_pi0.Rd
633084374def6537b3055b82906d9c3a *man/dfdr_plot_scope_disagreement_matrix.Rd
cc64acebe2d97c58a35a88e4134c2c1c *man/dfdr_plot_score_distributions.Rd
5fabf2f0d2b2bc43b64ffeb621c6aebd *man/dfdr_render_report.Rd
c630140857c68a0840131f69b0bdc422 *man/dfdr_run_all.Rd
e97b0f5c210d9492fc89a5ae4fbd33aa *man/dfdr_run_jaccard.Rd
676f1d7a489e7e4f2a83721f034f8fbf *man/dfdr_safe_filename.Rd
63c8b65194bdbbadfe37efead903153f *man/dfdr_scope_disagreement.Rd
c9f332b9251105a2b7df18e168055af1 *man/dfdr_summary_headline.Rd
ea178b56023281327f171ed3eaafd8ee *man/dfdr_sumpep.Rd
7efa9fc81182c8f192be8b3deede3471 *man/dfdr_write_manifest.Rd
fa5e71ed62ec640a22c6d9fb7f9187ec *man/dfdr_write_readme.Rd
2b83168c9c826fc55814cf5347b4c3ca *man/dfdr_write_report.Rd
986b5cc2a4c9775c395a9335fef97d66 *man/diann_detect_run_col.Rd
4de133e05bcf0ce06714bee697a30bfb *man/diann_global_minrunq.Rd
505bbbe4ba28b6b8b0bb7433d7b5c8e3 *man/diann_global_precursor.Rd
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2a8de2bd3df4352a30e3fd8364c4719d *man/diann_runxprecursor.Rd
db5b5a71cb84e1c432578cff85037bcb *man/dot-bh_threshold.Rd
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945d9d7992370fead044841475fc31bf *man/flag_headline.Rd
98f42035991777a6e7f8097ac7f20741 *man/jaccard_vec.Rd
46a51f6084840bc6a08dfe8f49d579e5 *man/mokapot_competed_universe.Rd
febc442255cccfd78db80897e6000a4f *man/mokapot_is_target_to_logical.Rd
e1c9d62d8d54d8c18ef17053d60ccc41 *man/mzid_parse_psms.Rd
4075e009394c6841a9450b76bbe77a36 *man/mzid_score_direction.Rd
1ed23319c9085ead443f1f7d32836de1 *man/mzid_to_internal_score.Rd
0157f9ffc0ca78500911470d20ae4c02 *man/print.dfdr_tbl.Rd
ba33dbe442d154f11947663b88a0f75c *man/read_dfdr_maxquant_msms.Rd
43896628edfe007ae9e19e41f6d31e42 *man/read_dfdr_mzid.Rd
3f153f6df9e7e56e744d56abf6dcc093 *man/read_diann_parquet.Rd
102e1d8cca2168a43c73f9548695515d *man/read_mokapot_psms.Rd
fd360f6544d2cc8914b96be1acb4532a *man/read_spectronaut.Rd
495bbf7c88e19f50002b1db00dea34ad *man/read_spectronaut_efficient.Rd
1fec625d2e05e55a8f518c409815b20e *man/safe_max.Rd
6e0b6ad4b1905f431491502b4bd84535 *man/safe_mean.Rd
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0e62c2954598d19f27fa39cd8c6be9ee *man/score_to_pvalue.Rd
befa798d1953b06d88a879b261478d82 *man/spectronaut_detect_run_col.Rd
f26035418f355ec15934bc2f1fffe0ca *man/spectronaut_parse_decoy.Rd
ff8d9c5bc5933b02181dc86838514c94 *man/spectronaut_recompute_q_from_score.Rd
250c41ad84ec390470893358440901f5 *man/spectronaut_require_cols.Rd
a3969e0a8d807d03dadf2567146e9fd0 *man/spectronaut_runxprecursor.Rd
72b3edacf25c72a723bc10400eb7e739 *man/tdc_qvalues.Rd
0d9412a1ce2c4f9ea7f0f83c539cfa2f *man/validate_dfdr_tbl.Rd
486851ef5b2ed6dfb82673ec76a37624 *man/wilson_ci.Rd
1f05a0bdf6d70ff8bef8d7d4c0e3decd *tests/testthat.R
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1a323a663124f6c7d22a5fd66e738d4a *tests/testthat/test-diann-pass.R
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1770ccda2d48490f5161c15575704ccb *tests/testthat/test-ipe-flags.R
20551869269120570b31206e118f1e2f *tests/testthat/test-pseudo-p.R
be779263b81277793026791caa6aa17d *vignettes/diann.Rmd
b688a6f0f22ad68ca856d18d33462afd *vignettes/maxquant.Rmd
2197e55e421b06f0efb7e33474680630 *vignettes/mokapot.Rmd
f6a85d0407e176f1b72f250e86a9d3c3 *vignettes/mzid.Rmd
a016737fd522f2b4358fec3a9c06bdf2 *vignettes/spectronaut.Rmd
