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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.pages namespace
  • webinterface.pages.utils package

webinterface.pages.utils package#

Utility modules for ProteoBench web interface.

Submodules#

  • webinterface.pages.utils.module_registry module
  • webinterface.pages.utils.submission_source module

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