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BioProfiling.jl\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/menchelab/RMP.jl/blob/master/LICENSE)\n[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://menchelab.github.io/BioProfiling.jl/dev/)\n[![CI](https://github.com/menchelab/BioProfiling.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/menchelab/BioProfiling.jl/actions/workflows/CI.yml)\n[![CI](https://github.com/menchelab/BioProfiling.jl/actions/workflows/NightlyCI.yml/badge.svg)](https://github.com/menchelab/BioProfiling.jl/actions/workflows/NightlyCI.yml)\n[![codecov](https://codecov.io/gh/menchelab/BioProfiling.jl/branch/master/graph/badge.svg?token=JE1KSLYYR6)](https://codecov.io/gh/menchelab/BioProfiling.jl)\n[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md) \n\nA flexible Julia toolkit for high-dimensional cellular profiles\n---\n\n## Introduction\n\nThis package allows to perform robust multidimensional profiling in 'Julia' and comes with helper functions, especially designed for high-content imaging-based morphological profiling.\n\n## Installation\n\n### Installation from Julia's package repository (easiest option)\n\nYou can simply add this package from the Julia repository like any other package:\n\n```julia\nimport Pkg\nPkg.add(\"BioProfiling\")\nusing BioProfiling\n```\n\n### Local installation\n\nAlternatively, you may use the following to load this package after cloning this repository:\n\n```julia\nimport Pkg\nPkg.activate(\u003cpathToThisFolder\u003e)\nusing BioProfiling\nPkg.activate()\n```\n\n### Installation from GitHub\n\nUse the following to install the package:\n\n```julia\nimport Pkg\nPkg.add(Pkg.PackageSpec(url = \"https://github.com/menchelab/BioProfiling.jl.git\"))\n```\n\nYou can then import the package normally:\n\n```julia\nusing BioProfiling\n```\n\n## Learn more\n\n* Have a look at the [documentation](https://menchelab.github.io/BioProfiling.jl/dev/)\n* Run our [example analysis notebooks](https://github.com/menchelab/BioProfilingNotebooks)\n* Check out the [JuliaCon 2021 poster](https://drive.google.com/file/d/1sjRONQ8dRJDGAiR-wBhC_rEBKiMIs5Rh/preview) presenting BioProfiling.jl \n* Read our [article published in Bioinformatics](https://doi.org/10.1093/bioinformatics/btab853)\n\n## Contribute\n\nWe welcome all sorts of contributions to this project! See our [contribution guidelines](CONTRIBUTING.md) and our [code of conduct](CODE_OF_CONDUCT.md) for more information.\n\n## Credits\n\nThis package was created by [Loan Vulliard](http://vulliard.loan) @ [Menche lab](https://menchelab.com/).  \nBioProfiling.jl relies on several amazing open-source Julia packages, listed in the requirement file (see [*Project.toml*](Project.toml)).  \nIf you use this tool in your research work, please cite [the article](https://doi.org/10.1093/bioinformatics/btab853) in which we detail how this tool is implemented and can be used:\n\n    BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations\n    Loan Vulliard, Joel Hancock, Anton Kamnev, Christopher W Fell, Joana Ferreira da Silva, Joanna I Loizou, Vanja Nagy, Loïc Dupré, Jörg Menche\n    Bioinformatics 2022; 38: 1692–9. DOI: https://doi.org/10.1093/bioinformatics/btab853\n\nWe also thank the reviewers whose suggestions contributed to improve the [example analyses](https://github.com/menchelab/BioProfilingNotebooks), their biological interpretation as well as the package in itself.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fbioprofiling.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmenchelab%2Fbioprofiling.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fbioprofiling.jl/lists"}