{"id":13680998,"url":"https://github.com/gygilab/Monocle","last_synced_at":"2025-04-30T02:34:04.386Z","repository":{"id":41047815,"uuid":"203456309","full_name":"gygilab/Monocle","owner":"gygilab","description":"Monocle is a tool for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments.","archived":false,"fork":false,"pushed_at":"2024-08-10T18:28:32.000Z","size":12120,"stargazers_count":8,"open_issues_count":3,"forks_count":6,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-08-10T19:56:58.720Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C#","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gygilab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-08-20T21:22:06.000Z","updated_at":"2024-08-10T19:56:58.721Z","dependencies_parsed_at":"2023-01-19T19:31:46.084Z","dependency_job_id":"c5c93803-901a-4f07-b3c4-3818ebce80ec","html_url":"https://github.com/gygilab/Monocle","commit_stats":null,"previous_names":[],"tags_count":58,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gygilab%2FMonocle","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gygilab%2FMonocle/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gygilab%2FMonocle/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gygilab%2FMonocle/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gygilab","download_url":"https://codeload.github.com/gygilab/Monocle/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224196554,"owners_count":17271855,"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":"2024-08-02T13:01:24.828Z","updated_at":"2024-11-12T00:30:37.781Z","avatar_url":"https://github.com/gygilab.png","language":"C#","funding_links":[],"categories":["4. Assorted pipeline Tools"],"sub_categories":["Table of Contents"],"readme":"# Monocle\n\nMonocle is a tool for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments.\n\nProject Folders:  \nMonocle - The class library project containing the core algorithm.  \nMonocle.CLI - The console application project.  \nMonocle.UI - The windows application project.  \nMonocle.Tests - The unit testing project.  \n\n*Authors*: Ramin Rad, Devin Schweppe  \nCopyright © 2019-2020 Gygi Lab and the above authors.  \nFor licensing (commercial and non-commercial) of **Monocle (including Monocle, Monocle.CLI, Monocle.UI, and Monocle.Tests)**, please contact the authors.\n\nFor the purposes of reading RAW data files:\nThe **RawFileReader** reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.\n\n### How to use the command-line application\nDownload the zip file from the latest release above, extract and navigate\nto it's contents.  Run the Monocle.CLI.exe file with the -f option to specify\nthe input file and the -t option to specify the output type. The output file\nwill be written in the same directory as the input file.\n\nThe following output types are supported:\n - csv\n - mzxml\n - mzml\n\nExample:\n\n    Monocle.CLI.exe -f x00123.raw -t csv\n\n### How to Build\nBuilds for the monocle library and the monocle cli app use the dotnet core command line.\n\n    # Run Tests in Monocle.Tests\n\tdotnet test\n\t\n    # Debug build\n    dotnet build\n\t\n\t# Build Release exe in Monocle.CLI\n\t# Use -r for the runtime that applies to you\n\tdotnet publish -c Release -r win10-x64\n\n### Monocle.CLI Option Information:\n\n    -f, --File                 Required. Input file for monoisotopic peak correction\n    \n    -n, --NumOfScans           The number of scans to average, default: +/- 6\n    \n    -a, --AveragingVector      Choose to average scans \"Before\" the parent scan, \"After\" or \"Both\" (default).\n\n    -c, --ChargeDetection      Toggle charge detection, default: false | F\n    \n    -z, --ChargeRange          Range for Charge Detection, if enabled. default: 2:6\n    \n    -u, --ChargesForUnknown    For low-res scans, output multiple precursors with these charges. default: 2:3\n    \n    -w, --ForceCharges         Output multiple precursors with charges set by -u even if charge is known. default: false\n    \n    -m, --MsLevel              Select the MS level at which monoisotopic m/z will be adjusted.\n    \n    -i, --UseMostIntense       Re-assign precursor m/z to the most intense peak in the isolation window.\n    \n    -q, --QuietRun             Do not display file progress in console.\n    \n    -t, --OutputFileType       Choose to output an mzXML \"mzxml\" or CSV file \"csv\".\n    \n    -o, --OutputFilePath       File to write. Include directory, filename, and extension\n    \n    --help                     Display this help screen.\n    \n    --version                  Display version information.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgygilab%2FMonocle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgygilab%2FMonocle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgygilab%2FMonocle/lists"}