{ "info": { "author": "Mark Ivanov & Lev Levitsky & Julia Bubis", "author_email": "pyteomics@googlegroups.com", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Scavager - a proteomics post-search validation tool\n---------------------------------------------------------------\n\nThe .pep.xml or .mzid files are required for basic operation of the script. Currently supported search engines:\nIdentipy, X!Tandem, Comet, MSFragger, msgf+, Morpheus.\n\n.fasta file is required for calculation NSAF (label-free quantitation index), protein sequence coverage and amino acid statistics.\n\nFor msgf+ and morpheus search engines it is desirable to provide cleavage rules used in search (These search engines do not report number of missed cleavages for peptides).\n\nThe output of Scavager contains:\n\n\n tab-separated table with unfiltered peptide-spectrum matches (ends with _PSMs_full.tsv)\n\n tab-separated table with identified peptide-spectrum matches at 1% PSM FDR (ends with _PSMs.tsv)\n\n tab-separated table with identified peptides at 1% peptide FDR (ends with _peptides.tsv)\n\n tab-separated table with identified proteins without grouping at 1% protein FDR (ends with _proteins.tsv)\n\n tab-separated table with identified protein groups at 1% protein FDR (ends with _protein_groups.tsv)\n\n png figure with PSM, peptide and protein features distributions\n\nInstallation\n-----\nUsing the pip:\n\n pip install Scavager\n\n\nUsage\n-----\nAlgorithm can be run with following command (works with Python2.7/Python3+):\n\n scavager path_to_pepXML/MZID\n\n OR\n\n scavager -h\n\nLinks\n-----\n\n- BitBucket repo & issue tracker: https://bitbucket.org/markmipt/scavager\n- Mailing list: pyteomics@googlegroups.com, markmipt@gmail.com\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://bitbucket.org/markmipt/scavager", "keywords": "", "license": "License :: OSI Approved :: Apache Software License", "maintainer": "", "maintainer_email": "", "name": "Scavager", "package_url": "https://pypi.org/project/Scavager/", "platform": "", "project_url": "https://pypi.org/project/Scavager/", "project_urls": { "Homepage": "https://bitbucket.org/markmipt/scavager" }, "release_url": "https://pypi.org/project/Scavager/0.1.9/", 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