{"id":13681052,"url":"https://github.com/statisticalbiotechnology/maracluster","last_synced_at":"2025-04-30T03:30:29.847Z","repository":{"id":41092648,"uuid":"45039905","full_name":"statisticalbiotechnology/maracluster","owner":"statisticalbiotechnology","description":"Matthew The's implementation of MaRaCluster","archived":false,"fork":false,"pushed_at":"2022-11-22T13:08:15.000Z","size":5007,"stargazers_count":11,"open_issues_count":4,"forks_count":3,"subscribers_count":19,"default_branch":"master","last_synced_at":"2024-11-12T00:36:19.168Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/statisticalbiotechnology.png","metadata":{"files":{"readme":"ReadMe.md","changelog":"ChangeLog","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-10-27T12:37:30.000Z","updated_at":"2023-07-20T04:54:40.000Z","dependencies_parsed_at":"2022-07-30T21:08:09.502Z","dependency_job_id":null,"html_url":"https://github.com/statisticalbiotechnology/maracluster","commit_stats":null,"previous_names":[],"tags_count":18,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statisticalbiotechnology%2Fmaracluster","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statisticalbiotechnology%2Fmaracluster/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statisticalbiotechnology%2Fmaracluster/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statisticalbiotechnology%2Fmaracluster/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statisticalbiotechnology","download_url":"https://codeload.github.com/statisticalbiotechnology/maracluster/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251634991,"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":"2024-08-02T13:01:25.529Z","updated_at":"2025-04-30T03:30:29.420Z","avatar_url":"https://github.com/statisticalbiotechnology.png","language":"C++","funding_links":[],"categories":["5. Raw Data Analysis"],"sub_categories":["Table of Contents"],"readme":"This repository holds the source code for clustering and merging of fragment spectra from shotgun proteomics experiments.\n\n## MaRaCluster\n\n### Installation\n\nInstallers for several operating systems can be found on the [Release page](https://github.com/statisticalbiotechnology/maracluster/releases). Both a command line as well as a graphical user interface are available for all platforms.\n\nIf you prefer to compile from source, or are running on a different operating system, [click here](#installation-from-source).\n\n### Example\n\nAn example, including spectrum files and a shell script, can be downloaded from http://kaell.org/files/maracluster_sample.zip.\n\n### Graphical User Interface (GUI)\n\nTo run the example, simply select the spectrum files after clicking the `Add ms2 files` button, select an output folder and click the `Run MaRaCluster` button.\n\nA more elaborate guide for using the GUI can be found from the Help menu in the menu bar of the GUI.\n\n### Command Line Interface (CLI)\n\nThe main functionality of MaRaCluster is provided by the `maracluster` command. This command has several sub-commands to execute different parts of the clustering and merging. The most important ones are `maracluster batch` and `maracluster consensus`. The first takes a list of ms2 spectra as input and outputs a list of clusters, the second takes one of these outputs and creates consensus spectra for each cluster.\n\nTo run `maracluster batch`, a flat text file with the absolute/relative path to each of the ms2 spectrum files (one per line) is needed. Such a file can easily be generated using a `ls -1` command, *e.g.* `ls -1 ms2/* \u003e files.txt` on Linux or `dir \u003cpath\u003e /b /s \u003e files.txt` on Windows. Any ms2 spectrum format readable by ProteoWizard can be used as input. Use the following command to start clustering:\n```\nmaracluster batch -b files.txt\n```\nThis will create several files called `MaRaCluster.clusters_p\u003cx\u003e.tsv` in a subdirectory called `maracluster_output`, for a range of p-value thresholds `10e-\u003cx\u003e`. These output files contain one spectrum per line, with different clusters separated by an empty line. The spectrum is listed with the path to the spectrum file in the first column, the unmerged scannr (or scan index if no scannr is available) in the second column and the cluster index in the third column, all separated by tabs.\n\nTo run `maracluster consensus`, we take one of the cluster files as input, e.g.:\n```\nmaracluster consensus -l maracluster_output/MaraCluster.clusters_p10.tsv\n```\n\nFor more information and options run `maracluster -h` on the command line.\n\n### Installation from source\n\nTo install MaRaCluster, you can use the provided installation script `./quickbuild.sh`, which will build the package in `./bin/build`, and install the executables in the `/usr/bin` folder (needs superuser rights). If you do not have superuser rights, or want to install the executable somewhere else, modify the script accordingly by setting the `-DCMAKE_INSTALL_PREFIX` flag to the desired location, and change the last line from `sudo make install` to `make install`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstatisticalbiotechnology%2Fmaracluster","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstatisticalbiotechnology%2Fmaracluster","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstatisticalbiotechnology%2Fmaracluster/lists"}