3f510515d220187b90854240186c3a7f *DESCRIPTION
90c4b9df76b8875fc6f5d78b2a1378bb *LICENSE
29d15ef1890672ac2b6386f5cd08420d *NAMESPACE
fbdfc30d7984db0bcdc9f2b247fa081d *NEWS.md
173c1a5437725d0c44f542ce02736224 *R/analyse_functional_network.R
8d7b23eada262e6da58093b8396b1389 *R/anova_protti.R
bdc935a13c2ef5b33349b9256010d578 *R/assign_missingness.R
9b75c43e9ec573b09367b16f0e66e40a *R/assign_peptide_type.R
eb50f18d60a443d9968640b4ce320917 *R/barcode_plot.R
faf899b42dba36b8dfda5cc8fb87ce00 *R/calculate_aa_scores.R
1b5d9ab89604294e8d5aba1bbfaaf5d6 *R/calculate_diff_abundance.R
ec9a803679dcfeb7d4edd2991c6450fd *R/calculate_go_enrichment.R
93594fa4fe21223f03a28ddc5740da7c *R/calculate_imputation.R
f86f2205d7335fc8b563a2ad855c1b41 *R/calculate_kegg_enrichment.R
0b02b5f1f0ad0a60a0d23814ee019495 *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
56c1651d64ba04fd6cbd35fa4b5f89bb *R/data.R
9f1de0d9efbdbba678f94343f71ddc7d *R/drc_4p.R
604fcaf6da9e0db8dc90fc7413571f75 *R/drc_4p_plot.R
e836b0d58cdd9e01ec36ad1c77533cdf *R/extract_metal_binders.R
58b8de8d2bb37203f8d168441bf4601a *R/fetch_alphafold_prediction.R
e9b0d406b76726880e607596b65775c1 *R/fetch_chebi.R
fa4d4f58321848c6af0ac4cfe7fe9ced *R/fetch_eco.R
fcbfaa9724ff2c349cb4e169d8de4d9c *R/fetch_go.R
8083814ef7f744d278d391fd45ba59fc *R/fetch_kegg.R
59016784b67470ca0204fd8de441f411 *R/fetch_metal_pdb.R
cc45b795243ff0302152858b8064feb0 *R/fetch_mobidb.R
413953ca9a9840b5be8d66e69a9c6e73 *R/fetch_pdb.R
38591cb2848890cfd4671698526790b9 *R/fetch_pdb_structure.R
f8d39070c3dac9cdea81d0d177d7402c *R/fetch_quickgo.R
84fec0229019e24900ef7a035bc2a5d9 *R/fetch_uniprot.R
a261f740d07289dfe0e5b6acd8cd6381 *R/fetch_uniprot_proteome.R
9ebefc68207e5d8d063bb6725443e4b0 *R/filter_cv.R
fff4bc227910b58c8e39e01a7d9a25cd *R/find_all_subs.R
1f556084b1e9e928cf33202b4285fff3 *R/find_chebis.R
047b837d2a6dfc7e8c2378fcc057c49a *R/find_peptide.R
a02030dae745b60947eacab3c750f280 *R/find_peptide_in_structure.R
b3b8277fcc9f22a64c8d0bd0e0bad00d *R/fit_drc_4p.R
fd954d510e32d3e3e47c7b0ecc0c8d9c *R/impute.R
21de198fc8ab818cac79266d5442c44d *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
828c04dc0b60249df98701d7c19c4f20 *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
601103138a39d19a33f32b0e63655a34 *R/qc_intensity_distribution.R
d054479b2a522dc37e0f2ed54c4abbe1 *R/qc_median_intensities.R
a2e6ba9a9ef803f4836be6f3579e00f7 *R/qc_missed_cleavages.R
1c056e65d951a449d88cf137f54e5c8d *R/qc_pca.R
377035bc1ee192f073c28eed9f98ccba *R/qc_peak_width.R
05dc31fcb1e67131e595034e3ba047cd *R/qc_peptide_type.R
9db3e8b22c1798262e9079decfb9b115 *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
b7a2db57548f9ae90f6f25254ccf0bab *R/split_metal_name.R
762b94523f9893e91fc0cee4ab4dc08f *R/try_query.R
dcd07936dd5594d27186b0b5377b3a9c *R/ttest_protti.R
19260bbac4c869a001350cf6a2450b5d *R/volcano_plot.R
82178f4941ea135bc5ced871688f9e70 *R/woods_plot.R
0e55c21cac1eb43c800f99ae20f8b696 *R/zzz.R
f3c2d4ba0f02746cd37c0f682357e69d *README.md
65bf9c94105bd28d60ade118093f0f92 *build/vignette.rds
863284fa45879a9cad22bd962ca2e85e *data/metal_chebi_uniprot.rda
2728bbfc48294d26971c3d5fc8a0d371 *data/metal_go_slim_subset.rda
065da0107f60cf897e1acefb7510d4fe *data/metal_list.rda
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
d2b8f9424713d831b7274fab70a88115 *inst/CITATION
56dbd3ce00be6ceff062f09dc1bd6fd1 *inst/doc/data_analysis_dose_response_workflow.R
05e454461c52c8d823a9fb8c8d15d587 *inst/doc/data_analysis_dose_response_workflow.Rmd
94f470a819f98e1ca77c01c3ad1f1d7f *inst/doc/data_analysis_dose_response_workflow.html
c9812595705406876735bfdc0d9f4f50 *inst/doc/data_analysis_single_dose_treatment_workflow.R
a941a5e2c3b8c9207ffe6a85a9924c98 *inst/doc/data_analysis_single_dose_treatment_workflow.Rmd
1d95592d29931f87ca13eddbf32d4a00 *inst/doc/data_analysis_single_dose_treatment_workflow.html
8310836ca6ec0ecda4a9b4544603ddbd *inst/doc/input_preparation_workflow.R
ba3925527b78834ad0a7262b33557fe1 *inst/doc/input_preparation_workflow.Rmd
22a386c17bda59a2ddb07e2fc1f91106 *inst/doc/input_preparation_workflow.html
e75376df9c3cf50cad2a2caf7ed325c8 *inst/doc/protein_structure_workflow.R
93d1336f15d19921c0202fcc56c3fddf *inst/doc/protein_structure_workflow.Rmd
da3d2fea895bee35569debb6b8890675 *inst/doc/protein_structure_workflow.html
993c6104a3103a0e3443b47c6b58e4d8 *inst/doc/quality_control_workflow.R
dd7fd30f4f27c8709dc013c78668b4cd *inst/doc/quality_control_workflow.Rmd
03d6242da323d1352a596e282b9879d3 *inst/doc/quality_control_workflow.html
3587da1a13aff45e0d0b1c29598a5a48 *man/analyse_functional_network.Rd
ea7dedb1da58e4f918566bf56e2ff7b1 *man/anova_protti.Rd
3e895ab87821187998488ac18349d6e8 *man/assign_missingness.Rd
f9de5009e784e461b52e6e106bbfa037 *man/assign_peptide_type.Rd
014bd6e31c9638e962cec70c5f0dd507 *man/barcode_plot.Rd
6a20c56face9e02c09e9a4a0a57f9453 *man/calculate_aa_scores.Rd
cc7b7dfa813fafedc5cec2675b77bd9b *man/calculate_diff_abundance.Rd
2f27a869ed1d84c56a201340cdbb3d70 *man/calculate_go_enrichment.Rd
b616e1906e24aa0c762ca81fba891d31 *man/calculate_imputation.Rd
e1ad8537f03aa65eab9d9038487ab196 *man/calculate_kegg_enrichment.Rd
c78ba3dd33d26d7a92506a8ea552b73b *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
dd204debb262ee1a73ef5cc3d56a56b5 *man/extract_metal_binders.Rd
4c80c1980fcde2943cee69071d46224f *man/fetch_alphafold_prediction.Rd
151c585e0b215c6cceedcf4318c266f3 *man/fetch_chebi.Rd
09000014e872a0300592b9f6f7c79152 *man/fetch_eco.Rd
9dc789b134aeecf96b6bd246809ce095 *man/fetch_go.Rd
e6c4985e83c2eaefdb3e2410da0aa74d *man/fetch_kegg.Rd
ba9606e5dd059e55ecbec2a8522afd58 *man/fetch_metal_pdb.Rd
5f6e3e8ca0ec6ed3ff75e04feff162f6 *man/fetch_mobidb.Rd
0fe3dcf82d4c681286573402ecc9cc33 *man/fetch_pdb.Rd
26012f46487512f04f155bbf4707eab7 *man/fetch_pdb_structure.Rd
0b05b8aa8d05d68deb14882f3aec00a2 *man/fetch_quickgo.Rd
ff657a6a5e326cc15c929f7c8ba8cc7c *man/fetch_uniprot.Rd
b358539514f17c806f9fd54cec475a93 *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
29f62c0c2360ef9de9a14dd8d2c216ea *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
f5c08ef728c12832c6662be787330b42 *man/metal_chebi_uniprot.Rd
ed88f8cf00399c86bfaf1697dbe243e7 *man/metal_go_slim_subset.Rd
844701c36a7373505432826420c83c70 *man/metal_list.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
77682d1df831ca19de336f4a162ee443 *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
96f2b1b13c3ec1352d08dcd4fa9a4f11 *man/qc_peak_width.Rd
b860375a7bffc4a847474e89e487beb1 *man/qc_peptide_type.Rd
648be00609887dc3a55a024284c7156d *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
039f25872181de2291dbe6e0a5e0e550 *man/split_metal_name.Rd
deab001d7afd13a6ec845195253f8bbb *man/treatment_enrichment.Rd
fc8d92cafd790ad644d2707104629e51 *man/try_query.Rd
5e240512045e00c12ffbe0ffa32b7ef7 *man/ttest_protti.Rd
18d9a47f3c2ab65b97b399f810f854da *man/viridis_colours.Rd
ce0342e6c8a2293c40cf1e28d1b88f13 *man/volcano_plot.Rd
69dd32ada8ceb004bf290d4a8912ca86 *man/volcano_protti.Rd
dedf687246cb8af166e2ff3a36dfab07 *man/woods_plot.Rd
cc3091e3e30cd5fcf36cc58738cf134a *tests/testthat.R
9dd22c09c92c113ddb3896bad107fa77 *tests/testthat/Rplots.pdf
c02d19555d74b55f531dcbca1e084d37 *tests/testthat/test-auxiliary_functions.R
74b4fc410a2e2521b1628333f2425608 *tests/testthat/test-fetch_extract_and_enrichment_functions.R
9ff10f9b7ef043ad43366c20e5cc8b2d *tests/testthat/test-qc_functions.R
8363b8511b995a6e27aa7f1f89b8342a *tests/testthat/test-queue_functions.R
b01794249210c8dae4bc1635195c0113 *tests/testthat/test-structure_functions.R
48fb3b61a2f7f60a5aac3d3b115f4f37 *tests/testthat/test-workflow.R
063f5d2b889fbaa0b918a2c9ac4433c8 *tests/testthat/test_import.csv
05e454461c52c8d823a9fb8c8d15d587 *vignettes/data_analysis_dose_response_workflow.Rmd
a941a5e2c3b8c9207ffe6a85a9924c98 *vignettes/data_analysis_single_dose_treatment_workflow.Rmd
c86d209b476935d956288103512d17b2 *vignettes/figures/interaction_2hwg.png
a2270d9fdbae8d52797ff36c2e038a23 *vignettes/figures/peptide_map_1zmr.png
78e2f7316937fbb0a1b55536a3792c7a *vignettes/figures/peptide_map_1zmr_score.png
ba3964d03d7c41182ac4f4b56df2ef27 *vignettes/figures/peptide_map_2hwg.png
5c7ecbdec8729376c311a972275e4e1c *vignettes/figures/peptide_map_2hwg_score.png
ba3925527b78834ad0a7262b33557fe1 *vignettes/input_preparation_workflow.Rmd
93d1336f15d19921c0202fcc56c3fddf *vignettes/protein_structure_workflow.Rmd
dd7fd30f4f27c8709dc013c78668b4cd *vignettes/quality_control_workflow.Rmd
