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Getting started
Development setup
Local usage
Modifying an existing module
Reviewing the submission of new data point
Changelog
Architecture and new modules
Layout of the Repository
Intermediate format specification
Adding a new module
Parameter homogenization
Submission validation
Python API
proteobench package
proteobench.datapoint package
proteobench.datapoint.datapoint_base module
proteobench.datapoint.denovo_datapoint module
proteobench.datapoint.entrapment_datapoint module
proteobench.datapoint.quant_datapoint module
proteobench.github namespace
proteobench.github.gh module
proteobench.io package
proteobench.io.params package
proteobench.io.params.adanovo module
proteobench.io.params.alphadia module
proteobench.io.params.alphapept module
proteobench.io.params.casanovo module
proteobench.io.params.contranovo module
proteobench.io.params.deepnovo module
proteobench.io.params.diann module
proteobench.io.params.fragger module
proteobench.io.params.i2masschroq module
proteobench.io.params.instanovo module
proteobench.io.params.maxdia module
proteobench.io.params.maxquant module
proteobench.io.params.metamorpheus module
proteobench.io.params.msaid module
proteobench.io.params.msangel module
proteobench.io.params.peaks module
proteobench.io.params.pihelixnovo module
proteobench.io.params.piprimenovo module
proteobench.io.params.pointnovo module
proteobench.io.params.proline module
proteobench.io.params.quantms module
proteobench.io.params.sage module
proteobench.io.params.spectronaut module
proteobench.io.params.wombat module
proteobench.io.parsing package
proteobench.io.parsing.parse_denovo module
proteobench.io.parsing.parse_ion module
proteobench.io.parsing.parse_peptidoform module
proteobench.io.parsing.parse_settings module
proteobench.io.parsing.utils module
proteobench.modules package
proteobench.modules.denovo package
proteobench.modules.denovo.denovo_DDA_HCD module
proteobench.modules.denovo.denovo_base module
proteobench.modules.entrapment package
proteobench.modules.entrapment.entrapment_base_module module
proteobench.modules.entrapment.entrapment_ion_DIA_Astral module
proteobench.modules.quant package
proteobench.modules.quant.benchmarking module
proteobench.modules.quant.quant_base_module module
proteobench.modules.quant.quant_lfq_ion_DDA_Astral module
proteobench.modules.quant.quant_lfq_ion_DDA_QExactive module
proteobench.modules.quant.quant_lfq_ion_DIA_AIF module
proteobench.modules.quant.quant_lfq_ion_DIA_Astral module
proteobench.modules.quant.quant_lfq_ion_DIA_Plasma module
proteobench.modules.quant.quant_lfq_ion_DIA_ZenoTOF module
proteobench.modules.quant.quant_lfq_ion_DIA_diaPASEF module
proteobench.modules.quant.quant_lfq_ion_DIA_lowinput module
proteobench.modules.quant.quant_lfq_peptidoform_DDA module
proteobench.modules.quant.quant_lfq_peptidoform_DIA module
proteobench.modules.rescoring package
proteobench.modules.rescoring.module_rescoring module
proteobench.modules.constants module
proteobench.plotting package
proteobench.plotting.plot_generator_base module
proteobench.plotting.plot_generator_denovo module
proteobench.plotting.plot_generator_entrapment module
proteobench.plotting.plot_generator_lfq_HYE module
proteobench.plotting.plot_generator_lfq_PYE module
proteobench.score package
proteobench.score.denovoscores module
proteobench.score.entrapmentscores module
proteobench.score.quantscoresHYE module
proteobench.score.quantscoresPYE module
proteobench.score.score_base module
proteobench.utils package
proteobench.utils.get_plots module
proteobench.utils.server_io module
proteobench.utils.submission module
proteobench.validation package
proteobench.validation.checks module
proteobench.validation.config module
proteobench.validation.context module
proteobench.validation.exceptions module
proteobench.validation.fasta module
proteobench.validation.profiles module
proteobench.validation.protein_ids module
proteobench.validation.report module
proteobench.validation.validator module
proteobench.exceptions module
webinterface package
webinterface.pages namespace
webinterface.pages.base_pages package
webinterface.pages.base_pages.tabs package
webinterface.pages.base_pages.utils package
webinterface.pages.base_pages.banner module
webinterface.pages.base_pages.base module
webinterface.pages.base_pages.denovo module
webinterface.pages.base_pages.entrapment module
webinterface.pages.base_pages.quant module
webinterface.pages.base_pages.tour_steps module
webinterface.pages.future_pages package
webinterface.pages.future_pages.6_Quant_LFQ_peptidoform_DIA_AIF module
webinterface.pages.texts package
webinterface.pages.texts.generic_texts module
webinterface.pages.texts.generic_texts_denovo module
webinterface.pages.texts.generic_texts_dia module
webinterface.pages.texts.proteobench_builder module
webinterface.pages.utils package
webinterface.pages.utils.module_registry module
webinterface.pages.utils.submission_source module
webinterface.pages.0_debug_session_state module
webinterface.pages.10_Quant_LFQ_DIA_ion_ZenoTOF module
webinterface.pages.11_Quant_LFQ_DIA_ion_Plasma module
webinterface.pages.12_Entrapment_DIA_ion_Astral module
webinterface.pages.2_Quant_LFQ_DDA_ion_QExactive module
webinterface.pages.3_Quant_LFQ_DIA_ion_AIF module
webinterface.pages.4_Quant_LFQ_DIA_ion_diaPASEF module
webinterface.pages.5_Quant_LFQ_DDA_peptidoform module
webinterface.pages.6_Quant_LFQ_DIA_ion_Astral module
webinterface.pages.7_denovo_DDA_HCD module
webinterface.pages.8_Quant_LFQ_DDA_ion_Astral module
webinterface.pages.9_Quant_LFQ_DIA_ion_lowinput module
webinterface.pages.base module
webinterface.Home module
webinterface.UI_utils module
webinterface.streamlit_utils module
Developer guide
webinterface package
webinterface.streamlit_utils module
webinterface.streamlit_utils module
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