40ce66fccf4467a22e2da1f5410fd9f1 *DESCRIPTION
90c4b9df76b8875fc6f5d78b2a1378bb *LICENSE
f1068834bb1e2bf2f2561d9c7c4e1c9a *NAMESPACE
12b576f0a1eb77b0bf9a2b625d6291ec *NEWS.md
8899b0d934419c9e0fc51eb3280bc18b *R/analyse_functional_network.R
8d7b23eada262e6da58093b8396b1389 *R/anova_protti.R
fdf03f56365e37ba4fc5ff0296dde10e *R/assign_missingness.R
9b75c43e9ec573b09367b16f0e66e40a *R/assign_peptide_type.R
eb50f18d60a443d9968640b4ce320917 *R/barcode_plot.R
faf899b42dba36b8dfda5cc8fb87ce00 *R/calculate_aa_scores.R
03f7ce04cea9f76a649c913a1a786ef5 *R/calculate_diff_abundance.R
7195cf52768d72c1e991fba581540644 *R/calculate_go_enrichment.R
93594fa4fe21223f03a28ddc5740da7c *R/calculate_imputation.R
925c3d4b1bdd46b76c61cdfeaca3de8b *R/calculate_kegg_enrichment.R
a597db15e96a4760a55771fefcc9ccd7 *R/calculate_protein_abundance.R
dc9a36bbc084dc12e2dc79292e9f25b4 *R/calculate_sequence_coverage.R
51aa4506f9788230d13d2357d0e0e8c0 *R/calculate_treatment_enrichment.R
a1e2b7a6dce651b9a56cb503dcb0fb8f *R/create_queue.R
5ae4481d3589d3aad84aab65b39018d8 *R/create_structure_contact_map.R
6904c4ae9ff108595dce1af1ce89e6c8 *R/create_synthetic_data.R
2e5917c28842f8ce441811e0ddec7b06 *R/data.R
9f1de0d9efbdbba678f94343f71ddc7d *R/drc_4p.R
604fcaf6da9e0db8dc90fc7413571f75 *R/drc_4p_plot.R
e7f5b13fca18d67be5e8d37104b01e20 *R/extract_metal_binders.R
48b55b616377a0add0b0a81ccaa5c3cd *R/fetch_alphafold_prediction.R
590a240c247ab3af01922ca8aebeb21c *R/fetch_chebi.R
0f9ae2358339dba4788167b25da7b106 *R/fetch_go.R
95f10eef85a97ddeb845869d0f1e4ac6 *R/fetch_kegg.R
97ee2148acb2becd08d4d4691e2fe2ee *R/fetch_metal_pdb.R
2cffacf7c88af51daf1d6e27accd338e *R/fetch_mobidb.R
89587079d3e368a8b28995c966b33154 *R/fetch_pdb.R
38591cb2848890cfd4671698526790b9 *R/fetch_pdb_structure.R
301d6fe92e684a717790892c99eaa9a7 *R/fetch_uniprot.R
5c93ed3521c1a3cbdb0420b1153fdcd6 *R/fetch_uniprot_proteome.R
9ebefc68207e5d8d063bb6725443e4b0 *R/filter_cv.R
9925733e828da479b7878ec482022824 *R/find_all_subs.R
689d8ae0171850bd211c18cc62cf7840 *R/find_chebis.R
047b837d2a6dfc7e8c2378fcc057c49a *R/find_peptide.R
ddcb48774704ef27b675fbdb2356d523 *R/find_peptide_in_structure.R
b3b8277fcc9f22a64c8d0bd0e0bad00d *R/fit_drc_4p.R
fd954d510e32d3e3e47c7b0ecc0c8d9c *R/impute.R
9f7b7894e1a2543d0512f066077b6a61 *R/map_peptides_on_structure.R
5bcbb7b68a59c1b96a3acad77a3de464 *R/normalise.R
4e4b71f28ce9eed1c48f131e7bae2568 *R/parallel_create_structure_contact_map.R
862803ca351ecfb89605a02f5124f936 *R/parallel_fit_drc_4p.R
575c1417d6cf61bc513489d0dd249160 *R/peptide_profile_plot.R
14ffa2b52d49188152b6d219b5a6307f *R/pval_distribution_plot.R
f7fa0cb1c1f6e61b494dbb35b6292c4c *R/qc_charge_states.R
be0d4d69e82ad50b5c0321e2416fbf48 *R/qc_contaminants.R
cc46d0d230abcc28c849f6cc3a282481 *R/qc_cvs.R
7d072c83c391b5ee38ac44b2873df4f0 *R/qc_data_completeness.R
a530f22681e3f8a0058386590ab76123 *R/qc_ids.R
4049ecf6cea6ca00e5099656b298cc3f *R/qc_intensity_distribution.R
d054479b2a522dc37e0f2ed54c4abbe1 *R/qc_median_intensities.R
a2e6ba9a9ef803f4836be6f3579e00f7 *R/qc_missed_cleavages.R
1c056e65d951a449d88cf137f54e5c8d *R/qc_pca.R
d07faf320dc6dd9f4c79a601617a0149 *R/qc_peak_width.R
05dc31fcb1e67131e595034e3ba047cd *R/qc_peptide_type.R
469846de240b56a80e5cfd073fd32a93 *R/qc_proteome_coverage.R
fb205c9fdd2cfb4548028d3ece8f1ad3 *R/qc_sample_correlation.R
b49836096d0ee1db06ccdd8a0b932446 *R/qc_sequence_coverage.R
ca9c30440e45fc7769f11a0486700fd2 *R/randomise_queue.R
2f48b0c08f7bb7b33eac8f6908aa3918 *R/read_protti.R
f3729666a151d356e2a55e25903061a5 *R/replace_identified_by_x.R
fca8ff052dd761a56d7c1c7bb407c0fd *R/scale_protti.R
d004dffb5958986549a301474d58aad9 *R/split_metal_name.R
ae945ecd1715846d235f6484c8e5a418 *R/try_query.R
dcd07936dd5594d27186b0b5377b3a9c *R/ttest_protti.R
9f4774973a6a72e26b641469f4de4d61 *R/volcano_plot.R
82178f4941ea135bc5ced871688f9e70 *R/woods_plot.R
0e55c21cac1eb43c800f99ae20f8b696 *R/zzz.R
3d38fd8c4721ed8c30c5bf2ff7616d06 *README.md
ac612e084b8664b89b50fa3234092953 *build/vignette.rds
4b363c993dfed46027455c195bfb7242 *data/protti_colours.rda
0b2ac2fbc28cb1a40dce7ff3a8a95f9b *data/ptsi_pgk.rda
3b855c61e660b4a28a1e82b95f5ee49f *data/rapamycin_10uM.rda
56fa120ca980cd2497fddb36aaae5bc0 *data/rapamycin_dose_response.rda
31adf1cf2e7d037b1bb8356727dae59a *data/viridis_colours.rda
c02a13e4ca1452779df19cf8f30019a7 *inst/doc/data_analysis_dose_response_workflow.R
19642918dd31bd1a291e9c61bece43b3 *inst/doc/data_analysis_dose_response_workflow.Rmd
cc631a590280d655c685e14b07c80e62 *inst/doc/data_analysis_dose_response_workflow.html
1ce3440745a11519bd1fe544ce7caebc *inst/doc/data_analysis_single_dose_treatment_workflow.R
b669d6666fce687d9a59c7eb77d898be *inst/doc/data_analysis_single_dose_treatment_workflow.Rmd
b73f48e1df9cdd66364e506bf70d77f7 *inst/doc/data_analysis_single_dose_treatment_workflow.html
8310836ca6ec0ecda4a9b4544603ddbd *inst/doc/input_preparation_workflow.R
8b8b3754822b548810c1268b963712aa *inst/doc/input_preparation_workflow.Rmd
358697161700b01eb7c80e604c9912bf *inst/doc/input_preparation_workflow.html
993c6104a3103a0e3443b47c6b58e4d8 *inst/doc/quality_control_workflow.R
82dcb3aba1f084d72f55b3739dcd33b4 *inst/doc/quality_control_workflow.Rmd
bb15acb0a35e4478b005a83ec44d07aa *inst/doc/quality_control_workflow.html
15550c7b42124754e079640cca70c9f1 *man/analyse_functional_network.Rd
ea7dedb1da58e4f918566bf56e2ff7b1 *man/anova_protti.Rd
a69eccea7a7439fae083d7ca5c68ecca *man/assign_missingness.Rd
f9de5009e784e461b52e6e106bbfa037 *man/assign_peptide_type.Rd
014bd6e31c9638e962cec70c5f0dd507 *man/barcode_plot.Rd
6a20c56face9e02c09e9a4a0a57f9453 *man/calculate_aa_scores.Rd
2f246bc9edf124af236e4f36a85607c1 *man/calculate_diff_abundance.Rd
fc783f92b5380ef5fc641529a1bd9d76 *man/calculate_go_enrichment.Rd
b616e1906e24aa0c762ca81fba891d31 *man/calculate_imputation.Rd
5bb88a00183a8b966e3257055a0e035c *man/calculate_kegg_enrichment.Rd
d4dbcc36d929f8bcd19fffec837e448b *man/calculate_protein_abundance.Rd
50da64cad1d8db86ec8a18be5c20344b *man/calculate_sequence_coverage.Rd
8f193c89d71d5ff6e78b237b7414b534 *man/calculate_treatment_enrichment.Rd
cb7e7f5f73dbedc3c391e18907a285cb *man/create_queue.Rd
16ba62f58f8ce2907a458ed18daf3b6e *man/create_structure_contact_map.Rd
80e0ee9d0fe651a2dc2ed760eab9a292 *man/create_synthetic_data.Rd
ee7e4337f8a7f11600f02766d783687b *man/diff_abundance.Rd
27539e05dadd40d5cf741ff0369eb1d1 *man/drc_4p.Rd
6413e07044170c208b590653d0983e4f *man/drc_4p_plot.Rd
687d7c1c90112159df98ab2422ead72d *man/extract_metal_binders.Rd
4c80c1980fcde2943cee69071d46224f *man/fetch_alphafold_prediction.Rd
2262ceb2cb7d2abfea0a7acc4429b387 *man/fetch_chebi.Rd
9dc789b134aeecf96b6bd246809ce095 *man/fetch_go.Rd
e6c4985e83c2eaefdb3e2410da0aa74d *man/fetch_kegg.Rd
ba9606e5dd059e55ecbec2a8522afd58 *man/fetch_metal_pdb.Rd
5f6e3e8ca0ec6ed3ff75e04feff162f6 *man/fetch_mobidb.Rd
c802033e2d475c2869d4e580b00ba765 *man/fetch_pdb.Rd
26012f46487512f04f155bbf4707eab7 *man/fetch_pdb_structure.Rd
ceef27e20e5e786b861148a1c72e06a2 *man/fetch_uniprot.Rd
98a4b9fc6dbbc2e70f84978546bf97e1 *man/fetch_uniprot_proteome.Rd
6b760e1c55a7c760a8304e6d818ba6f6 *man/figures/README-volcano-1.png
cb1e46f469cfbbbde29c8b5113e1d789 *man/figures/lifecycle-archived.svg
c0d2e5a54f1fa4ff02bf9533079dd1f7 *man/figures/lifecycle-defunct.svg
a1b8c987c676c16af790f563f96cbb1f *man/figures/lifecycle-deprecated.svg
c3978703d8f40f2679795335715e98f4 *man/figures/lifecycle-experimental.svg
952b59dc07b171b97d5d982924244f61 *man/figures/lifecycle-maturing.svg
27b879bf3677ea76e3991d56ab324081 *man/figures/lifecycle-questioning.svg
53b3f893324260b737b3c46ed2a0e643 *man/figures/lifecycle-stable.svg
1c1fe7a759b86dc6dbcbe7797ab8246c *man/figures/lifecycle-superseded.svg
87c69aa982d9f50408e8855a9d650798 *man/figures/protti_logo.png
7cf7ca522ef87119d768a12272ece700 *man/filter_cv.Rd
b905488e259e86dddc366cfca99cbc66 *man/find_all_subs.Rd
12a8304c6db535ac63f0926bf37a7a88 *man/find_chebis.Rd
1560446b173249bf3860631e25b258a5 *man/find_peptide.Rd
2a944475bbf2fec1894167e6ee6b0c66 *man/find_peptide_in_structure.Rd
3a1f348c61941018bfe923b6228b3f84 *man/fit_drc_4p.Rd
5ca5ff269466ad5669b752c0b169512e *man/go_enrichment.Rd
b7983f8facf5c2844fdc38bde9fa9193 *man/impute.Rd
3068ee1d5c08690a0945f58788be6e6a *man/kegg_enrichment.Rd
baa73af433a2831df629d5376aa00098 *man/map_peptides_on_structure.Rd
ab19c609437a34d2d457f8d1be053109 *man/median_normalisation.Rd
5cc859e766db3191bec26e6cf79c2cef *man/network_analysis.Rd
f3d863c5f16327a08d9d0fe0b5d265dd *man/normalise.Rd
2d2f00a1a29ccfa78269a5c1e41526cb *man/parallel_create_structure_contact_map.Rd
554b04f7c1e79011bcd5d08345580c31 *man/parallel_fit_drc_4p.Rd
86a1fe3acaea35715ddaeb9a45ee0480 *man/peptide_profile_plot.Rd
bb6c046678062b11b36a155561902e7c *man/peptide_type.Rd
ba80c889458279bb5d1e7c7cf4c8a893 *man/plot_drc_4p.Rd
ec4b7b924edfbe511b150db15f0745e6 *man/plot_peptide_profiles.Rd
7486d5037e02cec5aae28bafe76c97a6 *man/plot_pval_distribution.Rd
a22ff7562ff0c43b14cf0e3cdf2aa41f *man/protti_colours.Rd
3afef0d9d6588cf34a8c279c5f7624b1 *man/ptsi_pgk.Rd
1a386946339ce565582283bf58c2bb26 *man/pval_distribution_plot.Rd
36a33b534b0667864d81233222907fac *man/qc_charge_states.Rd
377345686ebf7c1ef928c0a1defcda98 *man/qc_contaminants.Rd
4eda8024ab2e673824340133c7df84f7 *man/qc_cvs.Rd
40298617f19379d3fd6831d93fa02fb7 *man/qc_data_completeness.Rd
33fc66c35c35abf3d6bdb93969fc71ea *man/qc_ids.Rd
f0e03440cd9724ed6c50d77d6bcccd36 *man/qc_intensity_distribution.Rd
79f0d2dfa0786c0ccfb1efc89f089ccb *man/qc_median_intensities.Rd
8768b435ab88b37f714cd99452377ee7 *man/qc_missed_cleavages.Rd
a66b60a77fe99025c99e823b42f571d2 *man/qc_pca.Rd
f44e81a3f99bdecd7e2546078f3a3b05 *man/qc_peak_width.Rd
b860375a7bffc4a847474e89e487beb1 *man/qc_peptide_type.Rd
5afa370b663e99acac8e23e1f2ff383a *man/qc_proteome_coverage.Rd
4e056ef17a2d612fe34e068a1eba62ce *man/qc_sample_correlation.Rd
dca79ad69b078a631cde0d4a9aa5f2c4 *man/qc_sequence_coverage.Rd
f4c3e624cddda27333951b67ced3c66d *man/randomise_queue.Rd
c2b648d12a7b5acb1e009e7314636ef0 *man/rapamycin_10uM.Rd
24a4ceb2e35dda6466f42cc94070bac5 *man/rapamycin_dose_response.Rd
bea08fd8507a7098faef43e57df4fac7 *man/read_protti.Rd
9fc6277e8647ef60f1b7a736bbf2b5bb *man/replace_identified_by_x.Rd
0f1e618f4c8f6e21a1c231b6cfbca5fb *man/scale_protti.Rd
9a1b0c3adcfd5dc00db9fa69428ea120 *man/sequence_coverage.Rd
f762c7a67ddc2fe6ecab0fb91cc9d762 *man/split_metal_name.Rd
deab001d7afd13a6ec845195253f8bbb *man/treatment_enrichment.Rd
4d41b81dae29117e92284570b57167ef *man/try_query.Rd
5e240512045e00c12ffbe0ffa32b7ef7 *man/ttest_protti.Rd
18d9a47f3c2ab65b97b399f810f854da *man/viridis_colours.Rd
b6f1672f956ea365dc20ec01c5dcc761 *man/volcano_plot.Rd
69dd32ada8ceb004bf290d4a8912ca86 *man/volcano_protti.Rd
dedf687246cb8af166e2ff3a36dfab07 *man/woods_plot.Rd
cc3091e3e30cd5fcf36cc58738cf134a *tests/testthat.R
c02d19555d74b55f531dcbca1e084d37 *tests/testthat/test-auxiliary_functions.R
d9d21a5b8d9f286de6db165c47d1df4f *tests/testthat/test-fetch_extract_and_enrichment_functions.R
9ff10f9b7ef043ad43366c20e5cc8b2d *tests/testthat/test-qc_functions.R
8363b8511b995a6e27aa7f1f89b8342a *tests/testthat/test-queue_functions.R
b1038a30f2334a46273ca991cff32b57 *tests/testthat/test-structure_functions.R
42da3015eacdac2a6054d51067a51511 *tests/testthat/test-workflow.R
063f5d2b889fbaa0b918a2c9ac4433c8 *tests/testthat/test_import.csv
19642918dd31bd1a291e9c61bece43b3 *vignettes/data_analysis_dose_response_workflow.Rmd
b669d6666fce687d9a59c7eb77d898be *vignettes/data_analysis_single_dose_treatment_workflow.Rmd
8b8b3754822b548810c1268b963712aa *vignettes/input_preparation_workflow.Rmd
82dcb3aba1f084d72f55b3739dcd33b4 *vignettes/quality_control_workflow.Rmd
