{"id":21280627,"url":"https://github.com/borgwardtlab/maldi_pike","last_synced_at":"2025-07-11T10:32:31.362Z","repository":{"id":42181846,"uuid":"237381630","full_name":"BorgwardtLab/maldi_PIKE","owner":"BorgwardtLab","description":"Code for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'","archived":false,"fork":false,"pushed_at":"2022-04-11T17:58:15.000Z","size":210,"stargazers_count":7,"open_issues_count":0,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2023-06-29T19:35:30.957Z","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-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BorgwardtLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"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":"2020-01-31T07:33:44.000Z","updated_at":"2023-01-30T16:23:39.000Z","dependencies_parsed_at":"2022-08-12T08:50:22.807Z","dependency_job_id":null,"html_url":"https://github.com/BorgwardtLab/maldi_PIKE","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2Fmaldi_PIKE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2Fmaldi_PIKE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2Fmaldi_PIKE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2Fmaldi_PIKE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BorgwardtLab","download_url":"https://codeload.github.com/BorgwardtLab/maldi_PIKE/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225715613,"owners_count":17512904,"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":"2024-11-21T10:37:44.213Z","updated_at":"2024-11-21T10:37:44.957Z","avatar_url":"https://github.com/BorgwardtLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# maldi_PIKE \u0026mdash; Peak Information KErnel for MALDI-TOF MS spectra\n\n`maldi_PIKE` is a small library for Python 3 that include the code used for \n'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass \nspectra'. The main method includes PIKE, the Peak Information KErnel for MALDI-TOF MS spectra, \nembedded in a Gaussian Process. We developed PIKE based on heat diffusion on structured \nobjects. It is well suited for MALDI-TOF mass spectra and able to capture interactions between\nmass peaks.\n\n# Dependencies\n\n- Python 3.7\n- packages listed in `pyproject.toml`\n\n# Installation\n\n- Clone the repository\n- `poetry install`\n\nFollow the instructions given by `poetry`.\n\n# Example behaviour of PIKE\n\nFigure 2:\n\n![PIKE_behaviour](PIKE_behaviour.png)\n\nCode to recreate this graphic in matplotlib can be found in\n`ismb2020_maldi/visualise_feature_map.py`. Use the script as\nfollows:\n\n```\npoetry run python ismb2020_maldi/visualise_feature_map.py data/Example_peaks.txt\n```\n\nThis should result in the following plot:\n\n![PIKE_behaviour_matplotlib](PIKE_behaviour_matplotlib.png)\n\nThis repository is work in progress.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fmaldi_pike","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fborgwardtlab%2Fmaldi_pike","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fmaldi_pike/lists"}