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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
  • Adding a new module

Python API

  • proteobench package
    • proteobench.datapoint namespace
      • proteobench.datapoint.quant_datapoint module
    • proteobench.github namespace
      • proteobench.github.gh module
    • proteobench.io package
      • proteobench.io.params package
        • proteobench.io.params.alphadia module
        • proteobench.io.params.alphapept module
        • proteobench.io.params.diann module
        • proteobench.io.params.fragger module
        • proteobench.io.params.i2masschroq module
        • proteobench.io.params.maxdia module
        • proteobench.io.params.maxquant module
        • proteobench.io.params.msaid module
        • proteobench.io.params.msangel module
        • proteobench.io.params.peaks 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_ion module
        • proteobench.io.parsing.parse_peptidoform module
        • proteobench.io.parsing.parse_settings module
        • proteobench.io.parsing.utils module
    • proteobench.modules package
      • proteobench.modules.quant package
        • 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_diaPASEF module
        • proteobench.modules.quant.quant_lfq_ion_DIA_singlecell 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 namespace
      • proteobench.plotting.plot_quant module
    • proteobench.score package
      • proteobench.score.quant package
        • proteobench.score.quant.quantscores module
    • proteobench.utils package
      • proteobench.utils.get_plots module
      • proteobench.utils.server_io module
      • proteobench.utils.submission module
    • proteobench.exceptions module
  • webinterface package
    • webinterface.pages package
      • webinterface.pages.base_pages package
        • webinterface.pages.base_pages.quant module
      • webinterface.pages.future_pages package
        • webinterface.pages.future_pages.6_Quant_LFQ_DIA_ion_singlecell module
        • 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_dia module
        • webinterface.pages.texts.proteobench_builder 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.8_Quant_LFQ_DDA_ion_Astral module
    • webinterface.Home module
    • webinterface.streamlit_utils module
  • Developer guide
  • proteobench package

proteobench package#

ProteoBench.

Subpackages#

  • proteobench.datapoint namespace
    • Submodules
      • proteobench.datapoint.quant_datapoint module
        • QuantDatapoint
        • filter_df_numquant_epsilon()
        • filter_df_numquant_nr_prec()
  • proteobench.github namespace
    • Submodules
      • proteobench.github.gh module
        • GithubProteobotRepo
  • proteobench.io package
    • Subpackages
      • proteobench.io.params package
        • ProteoBenchParameters
        • Submodules
      • proteobench.io.parsing package
        • Submodules
  • proteobench.modules package
    • Subpackages
      • proteobench.modules.quant package
        • Submodules
      • proteobench.modules.rescoring package
        • Submodules
    • Submodules
      • proteobench.modules.constants module
  • proteobench.plotting namespace
    • Submodules
      • proteobench.plotting.plot_quant module
        • PlotDataPoint
  • proteobench.score package
    • Subpackages
      • proteobench.score.quant package
        • Submodules
  • proteobench.utils package
    • Submodules
      • proteobench.utils.get_plots module
      • proteobench.utils.server_io module
      • proteobench.utils.submission module
        • get_submission_dict()

Submodules#

  • proteobench.exceptions module
    • ConvertStandardFormatError
    • DatapointAppendError
    • DatapointGenerationError
    • IntermediateFormatGenerationError
    • ParseError
    • ParseSettingsError
    • PlotError
    • ProteobenchError
    • QuantificationError

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