{"id":13681059,"url":"https://github.com/white-lab/pyproteome","last_synced_at":"2025-04-30T03:30:30.297Z","repository":{"id":62582735,"uuid":"52630222","full_name":"white-lab/pyproteome","owner":"white-lab","description":"Python library for analyzing mass spectrometry proteomics data.","archived":false,"fork":false,"pushed_at":"2024-03-20T19:06:57.000Z","size":1711,"stargazers_count":13,"open_issues_count":0,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-16T03:17:56.502Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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/white-lab.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-02-26T20:16:58.000Z","updated_at":"2025-01-03T14:25:25.000Z","dependencies_parsed_at":"2024-08-02T13:20:00.087Z","dependency_job_id":"e184bf7c-7851-420b-ad3d-4ef26467e82f","html_url":"https://github.com/white-lab/pyproteome","commit_stats":{"total_commits":1391,"total_committers":2,"mean_commits":695.5,"dds":0.006470165348670065,"last_synced_commit":"1cad2963d60cc85943859e16c37c4eb1a329b6f0"},"previous_names":[],"tags_count":24,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/white-lab%2Fpyproteome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/white-lab%2Fpyproteome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/white-lab%2Fpyproteome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/white-lab%2Fpyproteome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/white-lab","download_url":"https://codeload.github.com/white-lab/pyproteome/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251634992,"owners_count":21619122,"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","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":"2024-08-02T13:01:25.659Z","updated_at":"2025-04-30T03:30:29.947Z","avatar_url":"https://github.com/white-lab.png","language":"Python","funding_links":[],"categories":["5. Raw Data Analysis"],"sub_categories":["Table of Contents"],"readme":"# pyproteome\n\n[![Build Status](https://img.shields.io/travis/white-lab/pyproteome.svg)](https://travis-ci.org/white-lab/pyproteome)\n[![Coverage Status](https://img.shields.io/coveralls/white-lab/pyproteome.svg)](https://coveralls.io/r/white-lab/pyproteome?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/pyproteome/badge/?version=latest)](https://pyproteome.readthedocs.io/en/latest/)\n[![Requirements Status](https://requires.io/github/white-lab/pyproteome/requirements.svg?branch=master)](https://requires.io/github/white-lab/pyproteome/requirements/?branch=master)\n[![PyPI](https://img.shields.io/pypi/v/pyproteome.svg)](https://pypi.python.org/pypi/pyproteome)\n\n\nPython library for analyzing mass spectrometry proteomics data.\n\n## Installation\n\nTo install the core pyproteome python library, [install Python \u003e= 3.6](https://www.python.org/) and [the latest version of pip](https://pip.pypa.io/en/stable/installing/). Then run the following command:\n\n```\npip install pyproteome\n```\n\nTo install dependencies for [PHOTON](https://github.com/jdrudolph/photon), run the following command:\n\n```\npip install pyproteome[photon]\n```\n\n### Windows\n\nIf you are using Windows, it is easiest to use the latest version of\n[Anaconda](https://www.continuum.io/downloads) for your Python installation, as\npyproteome requires several hard-to-install packages, such as NumPy and SciPy.\n\nThen, you can simply run the above `pip install pyproteome` command to install\nthis package and the rest of its dependencies.\n\n### CAMV\n\npyproteome can use CAMV for data validation. If you have the executable\ninstalled on your system, simply add \"CAMV.exe\" to your system path and\npyproteome will locate it automatically.\n\n## Examples\n\nThere are several example analyses located in the [pyproteome-data\nrepository](https://github.com/white-lab/pyproteome-data/tree/master/examples).\n\nFor a full list of package functionality, refer to the\n[online documentation](https://pyproteome.readthedocs.io/en/latest/).\n\n## Directory Hierarchy\n\npyproteome expects a certain directory hierarchy in order to import data files\nand interface with CAMV. This pattern is as follows:\n\n```\nbase_directory/\n    CAMV Output/\n    Figures/\n    MS RAW/\n    Searched/\n```\n\nSee `pyproteome.paths` if you are using a custom directory hierarchy. i.e.:\n\n```\n\u003e\u003e\u003e from pyproteome import paths\n\u003e\u003e\u003e paths.MS_RAW_DIR = \"path/to/raw_files/\"\n\u003e\u003e\u003e paths.MS_SEARCHED_DIR = \"path/to/msf_files/\"\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwhite-lab%2Fpyproteome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwhite-lab%2Fpyproteome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwhite-lab%2Fpyproteome/lists"}