{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"alphapeptstats","owner":"MannLabs","isFork":false,"description":"Python Package for the downstream analysis of mass-spectrometry-based proteomics data","topicNames":["proteomics","mass-spectrometry","maxquant","dia-nn","fragpipe","alphapept-ecosystem","spectronaut","msfragger"],"topicsNotShown":0,"allTopics":["proteomics","mass-spectrometry","maxquant","dia-nn","fragpipe","alphapept-ecosystem","spectronaut","msfragger"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":8,"issueCount":17,"starsCount":48,"forksCount":12,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-24T10:46:45.057Z"}},{"type":"Public","name":"SPARCSpy","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":12,"starsCount":9,"forksCount":6,"license":null,"participation":[1,3,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,0,0,0,0,0,0,0,1,1,4,14,5,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-24T09:10:40.473Z"}},{"type":"Public","name":"SPARCStools","owner":"MannLabs","isFork":false,"description":"python tools to perform data parsing and image stitching on microscopy data","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":5,"starsCount":5,"forksCount":1,"license":"MIT License","participation":[1,2,1,5,3,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,7,2,5,0,0,0,0,0,0,0,0,0,0,1,0,12,3,2,0,1,0,1,1,0,0,0,1,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T15:39:16.401Z"}},{"type":"Public","name":"alphabase","owner":"MannLabs","isFork":false,"description":"Infrastructure of AlphaX ecosystem","topicNames":["python","infrastructure","proteomics","mass-spectrometry"],"topicsNotShown":0,"allTopics":["python","infrastructure","proteomics","mass-spectrometry"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":4,"issueCount":3,"starsCount":24,"forksCount":8,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T13:40:05.755Z"}},{"type":"Public","name":"alpharaw","owner":"MannLabs","isFork":false,"description":"An open-source Python package to unify raw MS data accession and storage.","topicNames":["data-storage","mass-spectrometry","raw-data","data-accession"],"topicsNotShown":0,"allTopics":["data-storage","mass-spectrometry","raw-data","data-accession"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":2,"issueCount":2,"starsCount":12,"forksCount":1,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-22T18:20:51.745Z"}},{"type":"Public","name":"alphapeptdeep","owner":"MannLabs","isFork":false,"description":"Deep learning framework for proteomics","topicNames":["proteomics","hla","python","machine-learning","deep-learning"],"topicsNotShown":0,"allTopics":["proteomics","hla","python","machine-learning","deep-learning"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":8,"starsCount":94,"forksCount":17,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-21T10:55:15.674Z"}},{"type":"Public","name":"timsrust","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":2,"starsCount":16,"forksCount":8,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-14T07:04:50.450Z"}},{"type":"Public","name":"OmicLearn","owner":"MannLabs","isFork":true,"description":"🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data","topicNames":["machine-learning","bioinformatics","proteomics","omics","transcriptomics","biomarker-discovery"],"topicsNotShown":0,"allTopics":["machine-learning","bioinformatics","proteomics","omics","transcriptomics","biomarker-discovery"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":29,"forksCount":17,"license":"Other","participation":[0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,5,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-05T16:08:17.616Z"}},{"type":"Public","name":"alphaviz","owner":"MannLabs","isFork":false,"description":"AlphaViz is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquired with Bruker instrument.","topicNames":["visualization","quality-control","mass-spectrometry","bruker"],"topicsNotShown":0,"allTopics":["visualization","quality-control","mass-spectrometry","bruker"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":8,"starsCount":29,"forksCount":2,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-24T07:16:29.749Z"}},{"type":"Public","name":"py-lmd","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":4,"starsCount":6,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-23T21:25:40.838Z"}},{"type":"Public","name":"directlfq","owner":"MannLabs","isFork":false,"description":"Fast and accurate label-free quantification for small and very large numbers of proteomes","topicNames":["python","bioinformatics","algorithms","proteomics","quantification","alphapept-ecosystem"],"topicsNotShown":0,"allTopics":["python","bioinformatics","algorithms","proteomics","quantification","alphapept-ecosystem"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":5,"starsCount":34,"forksCount":4,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-22T12:30:10.622Z"}},{"type":"Public","name":"alphapept","owner":"MannLabs","isFork":false,"description":"A modular, python-based framework for mass spectrometry. Powered by nbdev.","topicNames":["bioinformatics","proteomics","mass-spectrometry","alphapept-ecosystem"],"topicsNotShown":0,"allTopics":["bioinformatics","proteomics","mass-spectrometry","alphapept-ecosystem"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":5,"issueCount":18,"starsCount":160,"forksCount":29,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-19T15:51:13.109Z"}},{"type":"Public","name":"pydiaid","owner":"MannLabs","isFork":false,"description":"An open-source Python package for dia-PASEF methods with Automated Isolation Design (py_diAID) from the Mann Labs at the Max Planck Institute of Biochemistry.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":6,"starsCount":14,"forksCount":4,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T12:56:07.542Z"}},{"type":"Public","name":"PeptDeep-HLA","owner":"MannLabs","isFork":false,"description":"DL model to predict HLA peptide presentation","topicNames":["hla","peptidomics","immunopeptidomics","deep-learning"],"topicsNotShown":0,"allTopics":["hla","peptidomics","immunopeptidomics","deep-learning"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":13,"forksCount":5,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-31T09:59:33.328Z"}},{"type":"Public","name":"alphamap","owner":"MannLabs","isFork":false,"description":"An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.","topicNames":["gui","proteomics","mass-spectrometry","peptide-level","visualization","python"],"topicsNotShown":0,"allTopics":["gui","proteomics","mass-spectrometry","peptide-level","visualization","python"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":10,"issueCount":15,"starsCount":72,"forksCount":17,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-25T11:26:27.875Z"}},{"type":"Public","name":"structuremap_analysis","owner":"MannLabs","isFork":false,"description":"Analysis workflow for investigating the structural context of PTMs","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":9,"forksCount":6,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-08T11:50:06.466Z"}},{"type":"Public","name":"structuremap","owner":"MannLabs","isFork":false,"description":"Python package for investigating the structural context of PTMs","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":26,"forksCount":7,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-08T11:49:38.630Z"}},{"type":"Public","name":"SPARCS_pub_figures","owner":"MannLabs","isFork":false,"description":"Notebook and data to recreate figures from SPARCS manuscript","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-01T16:25:34.660Z"}},{"type":"Public","name":"MitoPhos","owner":"MannLabs","isFork":false,"description":"MitoPhos data analysis notebooks","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-20T21:07:26.162Z"}},{"type":"Public","name":"alphasynchro","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-05T16:00:11.218Z"}},{"type":"Public","name":"timspeak","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-05T15:18:56.102Z"}},{"type":"Public","name":"alphatims","owner":"MannLabs","isFork":false,"description":"An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.","topicNames":["python","cli","gui","dia","dda","mass-spectrometry","ms","ion-mobility","tof","max-planck-institute"],"topicsNotShown":3,"allTopics":["python","cli","gui","dia","dda","mass-spectrometry","ms","ion-mobility","tof","max-planck-institute","tims","lc-tims-msms","pasef"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":10,"issueCount":4,"starsCount":76,"forksCount":24,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-13T08:30:15.213Z"}},{"type":"Public","name":"slurm_scripts","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-12T13:24:40.929Z"}},{"type":"Public","name":"refquant","owner":"MannLabs","isFork":false,"description":"Reference-channel based quantification for mDIA data","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-08T16:24:18.912Z"}},{"type":"Public","name":"single-cell-DVP","owner":"MannLabs","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-01T11:22:32.545Z"}},{"type":"Public","name":"streamlit_peptide_overlay","owner":"MannLabs","isFork":false,"description":"An example streamlit application that allows plotting on a protein sequence.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-28T16:33:27.832Z"}},{"type":"Public","name":"DeepScore","owner":"MannLabs","isFork":false,"description":"The DeepScore Repository for the EuBIC 2023 Hackathon","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":1,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-19T10:13:07.214Z"}},{"type":"Public","name":"CKG","owner":"MannLabs","isFork":false,"description":"Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":15,"issueCount":30,"starsCount":404,"forksCount":93,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-08T12:01:19.879Z"}},{"type":"Public","name":"ReactomeGSApython","owner":"MannLabs","isFork":false,"description":"Python interface to Reactome's gene set enrichment analysis service","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-28T12:23:41.636Z"}},{"type":"Public","name":"Quality-Control-of-the-Plasma-Proteome","owner":"MannLabs","isFork":true,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":5,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-05T15:51:39.773Z"}}],"repositoryCount":39,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}