96f621a0b079dc137512075dc680536af1d02169a97d1956472b80cd317c3e0f  .gitattributes
f3410e6a463c7777136867833fb0532af4fcaf5fb7639c84f3307c86cda5128d  .github/workflows/docs.yml
12e92b5ab3090d9c0c7554c6eef942fc45f2912aed1f98fcf7983b5261223803  .github/workflows/publish.yml
ef65c3b87ebc42ea2b7ac3d55c6d3707606a416095a77e9e6110baf9b0f317ee  .github/workflows/validate.yml
5c35e804ebac097a766f062c628315761296817f6bff0c5c667edcdf093c0670  .gitignore
9e8b6f2533b7b69b77a938651c55085169257361ed5efb5a4b6bf3f1b7ca1abe  GITHUB_UPLOAD.md
32bfc418cc7486110a683dbd06d37226e1bc50ab66123e923debb749dbb3d709  LICENSE
170144214388bdc8327bb691da2fcff55a92ddcb5be2cd9648312c2a09a8e552  LICENSE_NOTES.md
cadbdd0bfe487d60fa705c026e57186332db3f48b3621dade8d91ee73b4355df  MANIFEST.in
459332c645241335999f57410bd6e311cd3074f390e43b5fc7560b7b7b5d28be  OUTPUTS.md
34ccb7df388d3e018d50992d7625850247249e4b13d5bd5129bcffa5d9b97577  PACKAGE_README.md
98d8dcfc8533f2aa42bc3433586b9127db741853c0997ebb42bb40de50ad7d65  README.md
5d1de36b29e67ab8c72a46cae46d7fd1a9211a876adf1868f9cf292e7e316f15  assets/cli_help.txt
1fce898e35fb58028769ffd04c25d82f20f8aec6841aaffbb90a8263c6ea2dec  assets/config.schema.json
8fba5396cc24c0d73b78748670e2abaa89676448498bccc2a8b65d63cfa7f5f2  assets/config_ui.html
749b5d220650e605ce7f630e292121821e113e2db438b01f16b6fc5e52f8b42e  assets/empty_study.json
d0b1e0efa82e7c8eb4de6a7fe65db87b94109cf15d2468433fff98a0fd97dc3b  assets/fragpipe_hla.workflow
573c24ea6bdf6fcff82538784f9e2b130e14ebbf4c4750160adfcd26cdb048c5  assets/fragpipe_lfq_mbr.workflow
53363c0037418c383ad8f5209ab7f7b294af153ed488a6e74a609674b8fb83ec  assets/setup.html
78ef9172e7eae6c162ca75a9f12a26ff5e9d192cff0e86d7ab1a2068d6ddcc46  assets/tool_versions.json
3d3aff2fac1a9f77d87314bc5d09696527fb0e7425992ac91ff174767e99cca1  docs/advanced_reference.md
bcb064a2a22da5fa3bb59633e7c181b8e80bae5da25d24f772206956e0c324be  docs/browser-analysis.vtt
72ead5bf24fc8e3245a5afb8db4b85415f7a0a9e27777c693072e46acf7ffc43  docs/continuation.md
f7e431a2d4202436b475cc0857533116e421d552b690274035eaabaf2f6c5b0b  docs/index.html
4e287749dd05de5286352430a1cfddf1eea77891117aaf2f4be0491af85a7d74  docs/installation.md
58adce192eb0193724829dc5dca512911bf88bcde83627c3b740140dfeb1ebd0  docs/outputs.md
b757ca206b48f2f718c824a7257819045c732fdd3aad3122c9c59efddf12c32f  docs/provider_workbooks.md
6fda8e3a10a8a9a362f9c5382ba31dd27fcef2a3db87c214e8acb695f5314667  docs/quick_start.md
817d18ae3bf2bc2b731c8adffe23e1348cbd947e764cb62b92eccb0ef638349d  docs/raw-dia-setup.vtt
cc7b4292f6bdeb188b634a6b697dee31f9e925ae43934d6d857701aff469e0ce  docs/setup.md
92a7274a8f4b33463618c97df54379a1beb81800256031f14c9196bb4e90fda9  docs/terminal-analysis.cast
8bb0c01905017ce676413b4dad59875f36aa07578f2039adcf16457f2832aa21  docs/terminal-analysis.txt
a235002f02a3094dd7bed2999511782f3a738f47870d5268d7a0026fbdd54d3b  docs/terminal-analysis.vtt
edd4a4b4471542f1f75da812a608b70a6eabd318f447be49520e3a2e6d192b29  docs/troubleshooting.md
968bc3a4b7b2a1601a72ad280af1b36cb96c53ff8a56823954aaa171015047b5  docs/videos.md
79d19a74216f89bbcf0e515a89058c79abe40557cf4e3e08ac35f1693d943ba8  envs/environment.yml
124fbb1a0e15cb9799a6a8c8320b74a29a9a56cc0ab1a2ab498ee898262dc2bc  envs/linux-64.lock.txt
8ca83243d4b7ce0851e7827331bf62ee09fce72e2483dfb6946201c2726de902  envs/r-environment.yml
689d6895052efd9ebafbbc6d55c9b5adca5f4032c7a148936894b7c7e15ca77a  examples/diapasef.json
c2d7a0209975c4f6e9899383cb8cffe934f7ceab0b8235957dde947def624c56  examples/diapasef_samples.tsv
e08f3947a1042b28211673fca0f9e60a0a0cba50c1451e8c4a9f6cbd44fd31f8  examples/quantification_matrix.csv
0ce4c193b1012472d053704510664b588211bab061647699a8b19ef3c229c036  examples/quantification_samples.csv
20e5dca09b27ea0b2cd97ef6cb22b017d3fdeeefe7080bdae5214e17dc4ff5a8  examples/run.json
65c4ad4974c91836a121b22f7f90b8a0d8d4b8b197690546439331e8be6e42f7  examples/service_quantification.csv
6270e742796d1d42ba781e10ffe0f0fdc8bf672e15e5dab5cde626269642f02b  main.nf
c1928a26d6ea424465f71a63a16fa383b827aa6b14ebcc8dc92b1c3204d41979  modules/diapasef/00_env.py
d4d95ae5a816f2f913a1b677fcf457233482d59cb4a64f6cdbfeb409876ad39b  modules/diapasef/01_prepare_samples.py
30ba94a9f857bee0601071acbe812e71aea92384b901ece4f1d3bd5c54cbe429  modules/diapasef/02_predict_library.py
2b424905e08f73e3c61a8305acae90179c4715c32385f50f0886aa35ffec3fd0  modules/diapasef/03_build_library.py
bc85646f951b0848f55bcbb4119be14f025cfd8ab27616ffc2b051d9c9acc10b  modules/diapasef/04_quantify_samples.py
4ee4dc19af5d2f55006a3a11d9779bc7289ee12b879568fd0d3047eb75c68613  modules/diapasef/05_count_proteins.py
0356819e0882873b42002b7e9a38679995d633eed43986a8c32ff6b8ace1f7f7  modules/diapasef/06_collect_results.py
de4016dcc4c70059b6cf5063a5ddf7ed94eda751bdfd4f5b43a11733c4893d2c  modules/diapasef/NOTICE.md
0016400c072d3730a13b51feb4b98a4c450832da53dd7757c3c69cdf7730103a  modules/diapasef/common.py
61d8e802ae86bf3a95a7613caa6aa1fbd6ed069ecee87a90c20cc133931bc1bf  modules/diapasef/main.nf
3c7547b02c41901b1dfec7a9c5e57f65a2b358ddf38402e72bae4df18cfd63f4  modules/diapasef/method.toml
a19fcad271d00a048cbf69c02ea6b36574b88e06fed12a1f5542a205f5244686  modules/diapasef/requirements-lock.txt
155d64abe86835801045805ca008faf9e81d9f819a735a12db778fff24190332  modules/diapasef/stub_prepare.py
bed16f262bf39fb7a81f327695cc26e87cee3fee10d1800b11859f81a9b5f36f  nextflow.config
dd4e701efe2f05f91ae4444dc1105a831f7555ad7dfbc2e7a7132ded6680b246  pipeline_lib/differential.R
880a1bd534696f2075cd28492737b3810e3cd127bbbca605e8e2bac77c2ff188  pipeline_lib/drug_interaction.R
7085cfce883c24686885b6242eead9539f05206dd658bde39d5637db58b13cb0  pipeline_lib/drug_interaction_models.R
c5c952db059605e92a01738dcd5f4065a00fac2058f80d74da02e37f41b32d9a  pipeline_lib/final_results.py
64c209e4c4b8e9de1910394647ce2665fd91b863fa1c1f922f2a79ddba43379e  pipeline_lib/immunopeptidomics.py
25f9d4ff85140a1743778ee4db69a2cc036b4e97bae874f8112a7779eb49f343  pipeline_lib/intensity_differential.R
ceacd99045d037436e1a55f94c227f323f2c361a0d532e7cf288f6d86455a377  pipeline_lib/matrix_catalog.py
f03a5cdb1c979eb11c6aa009f3be1184de1e2d2ec11a5ffec88c7d5c4e38f90f  pipeline_lib/optional_analyses.py
2c8116ccbf11063f6ebcba72b020c8199f73ca4e0f6abf89a5cf13bfcaa90b49  pipeline_lib/optional_statistics.py
6992cc6df5e603b0f544d66dec819f5094d2161ab401b8b09c709337d3eed4f7  pipeline_lib/pipeline.py
53548a606774210d67a0673bb0f6ed8a495ecd3b3a2582b52f223d4aa2b8b74c  pipeline_lib/ptm_counts.py
ec4380b03e6baec7823d2cb7143d96d9eb765dc22c50213b0676ac5e032e43bd  pipeline_lib/quantification.py
eb88cdc07d011e2534079de1fe41ab47e1b20a7f35b9b1792398786e9dd9f919  pipeline_lib/quantification_analysis.py
d3da33c1171aada19429bfadc566f526ea55ecc54e8ec228667afe5e9f8203b3  pipeline_lib/quantification_config.py
95f4b19a93012ef26891a1755c2aac855e3e47bc82bbf986565c7b606098a25c  pipeline_lib/quantification_import.py
ddf1017921ac6d9521e9007a45aef2ab53f8babeaa7033add5bfc0c752973a1b  pipeline_lib/reporting.py
5ed767a1f9bfda9ab5d6c5ecf61dcfc2a6dba2c9b6450b264a2ddd073fa33ae5  pipeline_lib/result_layout.py
0c8749bb983a74fbda0587a3f858c7751e9954208619131b2215f2d157514d6a  pipeline_lib/result_reports.py
39565d5a1d92cbff2f2322f9d841db2f4e11e6a95fb31bb3bc5f3e7eaefba5c4  pipeline_lib/results_dashboard.html
0811b13051c06e219bdcfd6e702308eeb549d2f5d28f5a1f659ee5a954eeada9  pipeline_lib/search_checkpoint.py
0bdb7aab1719f59f427c66bf2eb1095eab13b0fac87ddc37604cf4597ae88cbd  pyproject.toml
00817802157c1605359064cbccb1f8ad4a4e6e924d881c703def06b8d9c201af  scripts/analysis_modules.py
3e6507dabe28d8fe60ef266136e275324727f0a5e97e1b710d67c19edd7f4193  scripts/analyze_quantification.py
bf05c23290458e60c9d884407114d919668f24e2531b8ee60d736843b6b4b4d6  scripts/bootstrap_runtime.sh
c15a6bb21e2220d71ef1a1573a743a718df0d1a825b8f52fa8c717185a5918f5  scripts/config_server.py
8067bc587b1f56ed92873b1556b1e599e75e66b6b6cc21d99c77234580496bde  scripts/continue_folder.py
79d10d29f00e0c6279b94e623f14ff93f442c317b00896f944377d768c3402d5  scripts/continue_run.py
6d9a99739417d24fb089a16271f4f5803fc82582b226ce6b0dadb6f009d52b20  scripts/desktop_focus.py
a50e905a3f9bd785749be2d8aeadf1c3fc6c64d40494cef222fb7f77f7426059  scripts/dia_browser.py
b6b2bd47d48f6aadf06f234508765b3c64e2fc09877af67d29611ef6b18c7361  scripts/diapasef_config.py
bc6b64b45d7e5737852ae5990542658ce75aee44798e8ec522c0b706ea3230a9  scripts/differential_tools.py
3eab65a369f24bae1791e3a2c103b45b5b78443fd9901c5cf8e63a77c3d0d954  scripts/export_ptm_counts.py
543a03a6af6218a205e6de47f36b02527f088037293293e3887c12e2a9c3e7d1  scripts/fasta_download.py
d6dceb1f55d4ae6905ab3c5ea6f7eb091a8911a84b6b9d27bc677e283762924b  scripts/install_differential_tools.sh
d6b7f88318a22c0371b4ba351f3ed956933a18c4fb5c124c449162df739bdfc0  scripts/native_folders.py
710bfe928000b40ce036ac05fa0189ee1c82dd056b417e765b61ac0001d90b5b  scripts/package_source.py
64593c29021e5c0500e17fe6dbded40e56eef02e77227924515522b0045b56e5  scripts/proteomics_detection.py
62c99103aa62afcd32f4a9fccca32805f443b05df3b6ab1cb4c639a730820c13  scripts/reanalyze_counts.py
5d5dfcc826de97e6c5d4e38dcf3e0537e57f3add4976b2d5d03ff68104d4d8a9  scripts/reanalyze_dia.py
2ef2b6ac4c8f771c92ce9ab1c9236901d5a79f8f9b3342583b64c9e374c843f4  scripts/record_walkthroughs.py
143557a721bdd1eae97c314ca7333388cf16289014f98c455f680c796179df32  scripts/sample_detection.py
8d52f9b6bbd45819f600947d3bd019ea774cde9d0d613bd58d1157de20f3d603  scripts/setup_project.py
a1afff44765e514f95424dd3da714cccc30b123fd5a27d52bef0f6022beb3e92  scripts/stream_progress.py
4c6e339b5c63a591956b22ef3ec3fe9bf6cb2d9aa928a1866726830a68ec8584  scripts/system_capabilities.py
54c92cd80624c944a663e8348d838a04cf0a9ab0d737b5fc7e48243aa475ac47  scripts/tool_manager.py
eef87189c1890183f4a9d70df6444253a31663c826c60e863bb84347d5c19b1d  scripts/ui_log_follow.py
79704d50c39117e477c14fe182c044e0968eaed2c98121044004a01d7250f9f3  scripts/ui_run_state.py
cde579db85b1f8ce68eee8e7778d0858bdde13f3751d90211a84985142ef73ce  scripts/ui_runner.py
6638999f860ecbeaf42387ed0b1b217e2aea6393d52e735b1734c90edf23dd50  scripts/ui_server_lifecycle.py
408b818c090d3da75c5df5fd20f0acaab02f689f20c57c866893a5be72a96155  scripts/validate_distribution.py
32b8ef6e75b5ebcb853efe62ad0987d98fac94762d84b04bb93a55ceae827580  scripts/validate_repo.py
1c4f92c03720cbffa40214f20ce0e4b756ca77bf5b42f2f77c6bdc764940d324  setup_environment.sh
40c3232b873131fd06db7eba4a45d3301df37aeff252f206220838cd14b24365  src/fun_proteomics/__init__.py
79ee6f134c5c5193377cf9b189cbdcc3e2095e49ba9cec310114441c15a917c4  src/fun_proteomics/__main__.py
6ef29a1d097fc295d495820875940d664839c115867d8f98822e7f8c0145fd91  src/fun_proteomics/_build.py
242ea7070894f5791afc5df5211a30c2d2bee78d09c52eab29a83a20eb28f97e  src/fun_proteomics/assignments.py
e752c8b69adce730b97838650f3698824e43c35b428ef59deb42186ece384d29  src/fun_proteomics/cli.py
9f2da980806b23eb5be4241ca8f5ca22af0bed7d70264260d8308fad49622eeb  src/fun_proteomics/continuation.py
4a04a9518a27f090b4071842fbff5b93f3a04eedced72bbaabebd65e66aa88bb  src/fun_proteomics/project.py
6d52f04698a7905dcbd7e42f8532812b37de2e7b1f773367c33b80aa23e7d9f5  src/fun_proteomics/requirements.py
a9e55946abf51c513d5cdb358a498b69b5fdf7349429328caed931f9bfcbf288  src/fun_proteomics/setup_terminal.py
25efb8862e693117373b3c70af4ba8ced2c114a935eb78b74a2609aac60eb5aa  src/fun_proteomics/setup_web.py
c5c5e27d1d17bfb4734eab5460086712203355f711a84de0bc4bbd167468f8df  src/fun_proteomics/study.py
bf268bdc7b24cf5da9f37be01cf7f81e022993a199b5390f6f99b866c24f2dd4  tests/make_fixture.py
2acad6a5eac522abdae529b77ad01c8f8a74c2b25781256eb1724d6e9f7f3e33  tests/run_all.sh
87ddb61ffb210e1019658429c353bc9c29378393cd8e53af65c984739513da29  tests/run_assignment_browser.py
50e041f0e2262ae0b574845f9b1e41bb449c2ea49c0090c0e22e95df8d48f7e3  tests/run_diapasef_smoke.py
3a06082fccb5927971cd4943b3748bb53ac4392023894c126e075ea7c95fc556  tests/run_guided_smoke.py
eb0a2892931e90c99873aabe7851aefb96c3d580d55e818fc3a5ecb3e3f5ca0c  tests/run_package_smoke.py
12f5f410b2fec565d2b329e7c59eab3366776b89e505c1d0ee0aeeaec4ed9cfa  tests/run_provider_browser.py
c538d3f8ee2bfc10e93da3969fb9051bc4512921d8bdd634d66c180403ade683  tests/run_smoke.sh
9a677877f7011a16a22dc5cea7e10c28ca7c46b144f16c59c677c8fa99f5ad34  tests/test_analysis_modules.py
7e004cd7521f5c4b2686a1c4c15b85a06163903019fd51ca01c28cc7efbf2e19  tests/test_assignments.py
b374b516fe80fbf355b01610b2a510ba586c15276c9725eb53614b33cb727031  tests/test_bootstrap.py
9d40c9ccd6e3082603f9f082e23b3347208febeededf53f40650bbf8300a2d45  tests/test_continue.py
2fb44cc1f38520f55b5e5bd4183cfe0d4d6d3f8dc2ee536d2f049056dc32fec7  tests/test_count_filter_controls.py
3871faad808b30c1be3785bfbbe9021362cbf07d296ce516834af18b79a86119  tests/test_dia_browser.py
c11d3a3a5750f17f93950c3ac4b03c15d0cf9a928103de72dc5c81759a80d993  tests/test_dia_integration.py
d4c2a60b3e6c288f44b6450cec1393ba83ef58680d6a998b9b0f3f4c7050d3d1  tests/test_dia_reuse.py
b3d21dcdffed20ce1a0bd2cea9cf10eb97974eb2d276f6a33c34e88e855c1ad7  tests/test_diapasef_config.py
20c52c47e4a0aa0b5465b519f43cc8457ac33e13171032b7b30187865b3a9e3b  tests/test_differential.py
a29c456fa8f83ce8f928afd824e61f19d932198a9cdaf58a8378e9a9692ab241  tests/test_drug_interaction_methods.py
08d3e44789157e48e24be8cd32a44ba5bc757adc5b39b27e57bceec51ee8060f  tests/test_fasta_download.py
54a5dfbcb853060aa64be53329332a092314f3b9c893700d1eef5465201d2767  tests/test_final_results.py
e331c44a229a971e1a3f25374e646fa6761a64285efbc64c61f93daf712a2f19  tests/test_guided_setup.py
9941ece98d8fa14dc4ad18f076ed29ed3053c64b5e38bccc3e848d322ee116b1  tests/test_immunopeptidomics.py
3642a76ceb044eb4c9cb2f1c4e540bfa058a9adc6629a056e8749830541fface  tests/test_interface_launcher.py
9f426312d7216fcf1d8d44418f1db70b9e01ff1574a67b405b6868a05f441d65  tests/test_launch_progress.py
0e3e3213391c5f706f9685bd50fa368ed9e00671a13c7beeeec58aca43c2d277  tests/test_matrix_catalog.py
2a24fe0d8223133b0b62bfc8139faec647d82bdec7d36b2d71ab0266d68d402c  tests/test_native_folders.py
e90b0327b1c9ccb6a5ea2cddd1cf8881b660938681b1c04c6bd3431b1f5891ec  tests/test_optional_analyses.py
7d84fd951640e1116a7de4cc5d64bd1607cbaaaa9891e3fe24636509c517e9ff  tests/test_optional_setup.py
5f9a3f8fef184e377c44c27020babc0586f62c5a12a2a045e5b548200d3dadde  tests/test_optional_statistics.py
bf45e235518ea7b804040a246c1f7b8e26b0a01cdd9a3f9b5c98942736d9f46c  tests/test_package_cli.py
bd9620791af80f6f0d0ee0ec42fca362649edbefb6f95d21ce39b6961777e316  tests/test_pipeline.py
31564ec48df78fe7d552a9ebe3e62c9f975e1f33cb959c0c70fb0e6c4bf5c3f9  tests/test_portability.py
6e39821d3f9d5f0053dcabf54c5f37119fe78af22c88e00415de22cc14e3c809  tests/test_proteomics_detection.py
1027da6c0d1a0912d8638dfb41dbba970348070312a778af9f093bdbe23d09ce  tests/test_provider_workbooks.py
7d770fb735c964f95be9b2e11b805d8ff0c983d4d1ee3fdaae1b9aac45f25c20  tests/test_ptm_counts.py
46df4610b8f290f45cac71770d594f948e87ca086efddf9e038f0be16af2b598  tests/test_ptm_reporting.py
81257d18371c80cd17326f4d48ecd2d225788aee016ddf6f5219989b40d04691  tests/test_quantification.py
4afd683a8bf4a9d86eebb794ca0b357a368223321e453a4bd373e3c4b08e727c  tests/test_result_layout.py
67823daa311c77f69c6f01951bb78ee09ce2d158c317b6e6254fe80231d0c511  tests/test_result_reports.py
5049daccf098d045115dfb80c2722887854000147db833f228ec4d87c76a369e  tests/test_resume_detection.py
1f9b0efaf63783722c66c0770e50dd6aaea00b0a3fdb40bfc2b4eb3276028cb2  tests/test_run_detection.py
65d770bfd6d62b59112bb578e58684871189f2ccc96c87d9908ee3aeaff1ca81  tests/test_sample_detection.py
fa5379cb60216b2311afe80509e5830b36a1a12699f4e601b611c8e4cdcfdc19  tests/test_system_capabilities.py
2628e9fd5ef298d853e70316c29b11c1e72ad98f2129b363c0932125cd0a69bb  tests/test_tool_manager.py
40d94a6d87f05f5857a6a75a90d0494c7b26eaaa8f83b36017e8e7d411753738  tests/test_ui_connection.py
399361a2270de5e2601d3b78004b69ffb697aa3942d448013a7e0b5e8d17e1b9  tests/test_ui_log_follow.py
5c83021cd27c51d6d61b7f765d1b8db6e82c0b5d84918f6c93eb549df08670b3  tests/test_ui_run_logs.py
143f9db58db240bed6b389b931954aba51e386e58f3e797cd44330a15873ebef  tests/test_ui_run_recovery.py
5d9f3b1fdec292ae3b98df1fb44cea5a9a8d060b5366eff7350d7abb8b5573a2  tests/test_ui_server_lifecycle.py
50aadddada8ae3ff58ceff013b55830a2ee3a8174052df158675fd0ffe6531b8  tests/test_ui_session.py
