{"id":13681122,"url":"https://github.com/mfitzp/padua","last_synced_at":"2025-10-29T21:43:10.616Z","repository":{"id":57450241,"uuid":"65808298","full_name":"mfitzp/padua","owner":"mfitzp","description":"Proteomic Data Analysis with Python (pandas, scikit-learn, numpy, scipy)","archived":false,"fork":false,"pushed_at":"2023-07-06T21:23:06.000Z","size":2003,"stargazers_count":24,"open_issues_count":5,"forks_count":11,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-08-19T04:10:45.173Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mfitzp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-08-16T09:46:26.000Z","updated_at":"2025-06-26T15:39:47.000Z","dependencies_parsed_at":"2022-08-26T07:40:15.191Z","dependency_job_id":"a430ef37-68c4-414a-b8ca-5ae1de1717f3","html_url":"https://github.com/mfitzp/padua","commit_stats":{"total_commits":116,"total_committers":5,"mean_commits":23.2,"dds":0.1637931034482759,"last_synced_commit":"8b14bf4d2f895da6aea5d7885d409315bd303ec6"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mfitzp/padua","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfitzp%2Fpadua","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfitzp%2Fpadua/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfitzp%2Fpadua/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfitzp%2Fpadua/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mfitzp","download_url":"https://codeload.github.com/mfitzp/padua/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mfitzp%2Fpadua/sbom","scorecard":{"id":638812,"data":{"date":"2025-08-11","repo":{"name":"github.com/mfitzp/padua","commit":"8b14bf4d2f895da6aea5d7885d409315bd303ec6"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":1.7,"checks":[{"name":"Token-Permissions","score":-1,"reason":"No tokens found","details":null,"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Code-Review","score":0,"reason":"Found 0/30 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Dangerous-Workflow","score":-1,"reason":"no workflows found","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"SAST","score":0,"reason":"no SAST tool detected","details":["Warn: no pull requests merged into dev branch"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Pinned-Dependencies","score":-1,"reason":"no dependencies found","details":null,"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: BSD 2-Clause \"Simplified\" License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Vulnerabilities","score":0,"reason":"11 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: GHSA-6p56-wp2h-9hxr","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2020-73","Warn: Project is vulnerable to: PYSEC-2020-107 / GHSA-jjw5-xxj6-pcv5","Warn: Project is vulnerable to: PYSEC-2024-110 / GHSA-jw8x-6495-233v","Warn: Project is vulnerable to: PYSEC-2020-108","Warn: Project is vulnerable to: PYSEC-2023-102","Warn: Project is vulnerable to: PYSEC-2023-114"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-21T10:04:48.656Z","repository_id":57450241,"created_at":"2025-08-21T10:04:48.657Z","updated_at":"2025-08-21T10:04:48.657Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281705763,"owners_count":26547506,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-29T02:00:06.901Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-02T13:01:26.691Z","updated_at":"2025-10-29T21:43:10.588Z","avatar_url":"https://github.com/mfitzp.png","language":"Python","funding_links":[],"categories":["6. Stastical Analysis"],"sub_categories":["Table of Contents"],"readme":"![PaDuA](PaDuA.png)\n\nA Python package for Proteomic Data Analysis, offering processing and analysis of the output of proteomics software [MaxQuant](http://maxquant.org).\n\n# Installation\n\nPaDuA is available via the Python package index at [PyPi](http://pypi.org) and can be installed in the usual way with:\n\n    pip install padua\n    \nOnce installed the package is available for import using:\n\n    import padua\n    \nThe package is organised into multiple submodules for different purposes, eg.\n\n1. `io` for reading and writing both MaxQuant and Perseus format files (input/output)\n1. `filters` for filtering data by quality and features\n1. `process` incorporating experimental design, labels to index, expand-side-table (Perseus) and more\n1. `normalization` for performing normalisation methods, e.g. remove column median\n1. `annotations` adding annotation metadata for quantified proteins\n1. `analysis` performing simple analyses, e.g. column correlations\n1. `plots` standard plot outputs for overviews of data\n\n# What is it for?\n\nThe goal is to provide a simple scripting approach to replicate many of the common steps for interacting with the output\nof MaxQuant. Many of the steps implemented are based on similar steps used in the MaxQuant sister software \n[Perseus](http://141.61.102.17/perseus_doku/). While currently Perseus has more features, it has stability issues with\nthe larger datasets we are currently using. Having the processing steps implemented in Python allows for simple \nprocessing workflow scripts to be created and re-used.\n\n# Examples\n\nAn example Phosphoproteomic label-free-quantification workflow would be as follows:\n\n    import padua\n    df = padua.io.read_maxquant('Phospho (STY)Sites.txt')\n\n    df = padua.filter.filter_localization_probability(df)\n\n    df = padua.filter.remove_reverse(df)\n    df = padua.filter.remove_only_identified_by_site(df)\n    df = padua.filter.remove_potential_contaminants(df)\n\n    # Use standard Pandas dataframe manipulations to set an index\n    df.set_index('Proteins', inplace=True)\n    df = df.filter(regex='Intensity ')\n\n    df = df.process.expand_side_table(df)\n\n    # Remove the multiplicity column\n    df = df.filter(regex='Intensity ')\n\n    df = padua.process.apply_experimental_design(df, 'experimentalDesignTable.txt')\n\n    # The result of this step will be a multilevel index Class, Replicate\n    # built by matching sample labels using regex\n    indices = [\n        ('Class': '^(.*)_',\n        ('Replicate': '_(\\d)', \n    ]\n    df = padua.process.build_index_from_labels(df, indices)\n\n# Future\n\nProvided functions are based on our current requirements, but will be expanded in future. \n\n# License\n\nPaDuA is open source software and available under the BSD 2-clause (Simplified) license.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmfitzp%2Fpadua","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmfitzp%2Fpadua","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmfitzp%2Fpadua/lists"}