{"id":20074652,"url":"https://github.com/greenelab/cimr","last_synced_at":"2025-05-05T21:32:06.208Z","repository":{"id":53532945,"uuid":"147383910","full_name":"greenelab/cimr","owner":"greenelab","description":"tool for continuously integrated meta-resource","archived":false,"fork":false,"pushed_at":"2021-03-25T22:46:31.000Z","size":35965,"stargazers_count":1,"open_issues_count":3,"forks_count":2,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-11-01T10:16:10.365Z","etag":null,"topics":["continuous-integration","gene-expression","gtex","gwas","twas"],"latest_commit_sha":null,"homepage":"https://cimr.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/greenelab.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-09-04T17:34:27.000Z","updated_at":"2024-03-12T12:43:39.000Z","dependencies_parsed_at":"2022-08-20T12:20:23.114Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/cimr","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcimr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcimr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcimr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcimr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/cimr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224470631,"owners_count":17316704,"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":["continuous-integration","gene-expression","gtex","gwas","twas"],"created_at":"2024-11-13T14:53:15.909Z","updated_at":"2024-11-13T14:53:16.430Z","avatar_url":"https://github.com/greenelab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\n****\ncimr\n****\n\n\n***************************************\ncimr is not yet released for public use\n***************************************\n\n=====================================================\ncontinuous integration and analysis of complex traits\n=====================================================\n\n==========\nYoSon Park\n==========\n\n**Useful links**:\n`Source repository \u003chttps://github.com/greenelab/cimr\u003e`_ |\n`Issues \u0026 Ideas \u003chttps://github.com/greenelab/cimr/issues\u003e`_ |\n`Documentation \u003chttps://cimr.readthedocs.io\u003e`_ |\n`cimr-d \u003chttps://github.com/greenelab/cimr-d\u003e`_\n\n\n*cimr* (continuously integrated meta-resource) is a convenience tool\nfor continuous analyses of variant-based association results from\nGWAS (genome-wide association studies), eQTL (expression-quantitative\ntrait loci mapping) or other association studies. cimr aims to\nstreamline the pre-analysis processing steps, provide standardized\ninput files and automate scripting for standard downstream analyses.\n\n\n\n============\nInstallation\n============\n\n-----------------\nInstalling python\n-----------------\n\ncimr requires python :math: `\\ge` 3.6. Installation of data analysis bundles\nsuch as `miniconda \u003chttps://conda.io/miniconda.html\u003e`_ or\n`anaconda \u003chttps://www.anaconda.com/download/\u003e`_ are recommended and will\ninstall all python packages cimr depends on. However, all required python\npackages can be downloaded and installed with setup.py or requirements.txt\nprovided here.\n\n\n------------------\nInstalling git lfs\n------------------\n\ncimr-d and some functionalities in cimr may use\n`git large file storage (LFS) \u003chttps://git-lfs.github.com/\u003e`_ .\nSee how to install\n`git \u003chttps://www.atlassian.com/git/tutorials/install-git\u003e`_ .\n\n\nTo install git-lfs on Ubuntu, run::\n\n    curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash\n    sudo apt-get install -y git git-lfs\n    git-lfs install\n\n\nAlternatively, you can install git-lfs through conda::\n\n    conda install -c conda-forge git-lfs \u0026\u0026 git lfs install\n\n\n---------------\nInstalling cimr\n---------------\n\nYou can use pip to install the latest stable release of cimr::\n\n    pip3 install cimr\n\n\nIf you want to try out the nightly build of cimr at your own risk,\nclone the repository from git::\n\n    git clone https://github.com/greenelab/cimr.git\n    cd cimr\n    pip3 install -r requirements.txt\n    python3 setup.py build\n    python3 setup.py install\n\n\n\n=================\nAnalysis examples\n=================\n\n------------------------------------------------------------------------\nQuality assurance and processing of association summary statistics files\n------------------------------------------------------------------------\n\nYou can use cimr to standardize public datasets using a yaml file, e.g.::\n\n    # example.yaml\n\n    data_file:\n        description: \u003e-\n            Global Lipid Genetics Consortium GWAS results for high-density\n            cholesterol levels\n        location:\n            url: https://zenodo.org/record/3338180/files/HDL_Cholesterol.txt.gz\n            md5: 2b28816a0a363db1a09ad9a6ba1a6620\n        columns:\n            variant_id: panel_variant_id\n            variant_chrom: chromosome\n            variant_pos: position\n            rsnum: variant_id\n\n    data_info:\n        citation: 10.1038/ng.2797\n        data_source: http://lipidgenetics.org/\n        data_type: gwas\n        context: hdl cholesterol\n        build: b38\n        sample_size: 187167\n        n_cases: na\n        can_be_public: true\n\n    method:\n        name: linear regression\n        tool: PLINK;SNPTEST;EMMAX;Merlin;GENABEL;MMAP\n        website: \u003e-\n            http://zzz.bwh.harvard.edu/plink/download.shtml;\n            https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html;\n            https://genome.sph.umich.edu/wiki/EMMAX;\n            https://csg.sph.umich.edu/abecasis/Merlin/tour/assoc.html;\n            http://www.genabel.org/sites/default/files/html_for_import/GenABEL_tutorial_html/GenABEL-tutorial.html;\n            https://mmap.github.io/\n\n    contributor:\n        name: Contributor Name\n        github: contributorgithub\n        email: contributoremail@emaildomain.emailextension\n\n\n\nDetails can be found in the\n`cimr-d contributions.md \u003chttps://github.com/greenelab/cimr-d/blob/master/doc/contributing.md\u003e`_.\n\n\nOnce the yaml file is prepared, you can run cimr locally::\n\n    cimr processor -process -yaml-file example.yaml\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fcimr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fcimr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fcimr/lists"}