{"id":13680992,"url":"https://github.com/Roestlab/DIAlignR","last_synced_at":"2025-04-30T02:34:02.138Z","repository":{"id":54395369,"uuid":"149298343","full_name":"Roestlab/DIAlignR","owner":"Roestlab","description":"This is a R package for alignment of DIA mass-spec data","archived":false,"fork":false,"pushed_at":"2021-02-24T17:50:53.000Z","size":27748,"stargazers_count":11,"open_issues_count":2,"forks_count":5,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-06-18T02:31:31.806Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/Roestlab.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}},"created_at":"2018-09-18T14:04:26.000Z","updated_at":"2024-06-10T04:10:15.000Z","dependencies_parsed_at":"2022-08-13T14:20:46.030Z","dependency_job_id":null,"html_url":"https://github.com/Roestlab/DIAlignR","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Roestlab%2FDIAlignR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Roestlab%2FDIAlignR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Roestlab%2FDIAlignR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Roestlab%2FDIAlignR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Roestlab","download_url":"https://codeload.github.com/Roestlab/DIAlignR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":213678897,"owners_count":15622597,"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":"2024-08-02T13:01:24.714Z","updated_at":"2024-08-02T13:13:33.278Z","avatar_url":"https://github.com/Roestlab.png","language":"R","funding_links":[],"categories":["4. Assorted pipeline Tools"],"sub_categories":["Table of Contents"],"readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-dialignr/README.html)\n[![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/dialignr/dialignr)\n\n# DIAlignR\nDIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.\n\n[![Travis build status](https://travis-ci.org/shubham1637/DIAlignR.svg?branch=master)](https://travis-ci.org/shubham1637/DIAlignR)\n\n# Documentation\nFor documentation please see [our vignette](https://htmlpreview.github.io/?https://github.com/shubham1637/DIAlignR/master/vignettes/DIAlignR-vignette.html).\n\n# Developing C++ code\n```\ncd DIAlignR\nmkdir build \u0026\u0026 cd build\ncmake -B. -H.. \nmake clean \u0026\u0026 make \u0026\u0026 make test\nmake runTest3\ncd ..\n```\n\nDocumenting C++ code\n```\nsudo apt install doxygen doxygen-gui \nsudo apt install graphviz\ncd DIAlignR\ncd src\ndoxygen doc/Doxyfile\n```\n\n# Installing Rcompression\n`devtools::install_github(\"omegahat/Rcompression\")`\n\n# Citation\nIf you use the provided algorithms or the package, please cite our paper:\n\nGupta S, Ahadi S, Zhou W, Röst H. \"DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.\" Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: https://doi.org/10.1074/mcp.TIR118.001132 Epub 2019 Jan 31.\n\nCNPN 2018 Poster doi: https://doi.org/10.6084/m9.figshare.6200837.v1     \nHUPO 2018 Poster doi: https://doi.org/10.6084/m9.figshare.7121696.v2     \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FRoestlab%2FDIAlignR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FRoestlab%2FDIAlignR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FRoestlab%2FDIAlignR/lists"}