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https://github.com/menchelab/BioProfiling.jl

A flexible Julia toolkit for high-dimensional cellular profiles
https://github.com/menchelab/BioProfiling.jl

high-content-screening julia morphological-analysis

Last synced: about 2 months ago
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A flexible Julia toolkit for high-dimensional cellular profiles

Host: GitHub
URL: https://github.com/menchelab/BioProfiling.jl
Owner: menchelab
License: mit
Created: 2020-02-13T15:15:12.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2023-07-14T16:22:43.000Z (12 months ago)
Last Synced: 2024-05-03T10:18:34.198Z (about 2 months ago)
Topics: high-content-screening, julia, morphological-analysis
Language: Julia
Homepage:
Size: 352 KB
Stars: 13
Watchers: 5
Forks: 1
Open Issues: 17
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Lists

awesome-cytodata - BioProfiling.jl - Toolkit for filtering and curation of morphological profiles in Julia. (Software / Genetic Perturbations)

README

        # BioProfiling.jl

[![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)

[![](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/menchelab/RMP.jl/blob/master/LICENSE)

[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://menchelab.github.io/BioProfiling.jl/dev/)

[![CI](https://github.com/menchelab/BioProfiling.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/menchelab/BioProfiling.jl/actions/workflows/CI.yml)

[![CI](https://github.com/menchelab/BioProfiling.jl/actions/workflows/NightlyCI.yml/badge.svg)](https://github.com/menchelab/BioProfiling.jl/actions/workflows/NightlyCI.yml)

[![codecov](https://codecov.io/gh/menchelab/BioProfiling.jl/branch/master/graph/badge.svg?token=JE1KSLYYR6)](https://codecov.io/gh/menchelab/BioProfiling.jl)

[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md) 

A flexible Julia toolkit for high-dimensional cellular profiles

---

## Introduction

This package allows to perform robust multidimensional profiling in 'Julia' and comes with helper functions, especially designed for high-content imaging-based morphological profiling.

## Installation

### Installation from Julia's package repository (easiest option)

You can simply add this package from the Julia repository like any other package:

```julia

import Pkg

Pkg.add("BioProfiling")

using BioProfiling

```

### Local installation

Alternatively, you may use the following to load this package after cloning this repository:

```julia

import Pkg

Pkg.activate()

using BioProfiling

Pkg.activate()

```

### Installation from GitHub

Use the following to install the package:

```julia

import Pkg

Pkg.add(Pkg.PackageSpec(url = "https://github.com/menchelab/BioProfiling.jl.git"))

```

You can then import the package normally:

```julia

using BioProfiling

```

## Learn more

* Have a look at the [documentation](https://menchelab.github.io/BioProfiling.jl/dev/)

* Run our [example analysis notebooks](https://github.com/menchelab/BioProfilingNotebooks)

* Check out the [JuliaCon 2021 poster](https://drive.google.com/file/d/1sjRONQ8dRJDGAiR-wBhC_rEBKiMIs5Rh/preview) presenting BioProfiling.jl 

* Read our [article published in Bioinformatics](https://doi.org/10.1093/bioinformatics/btab853)

## Contribute

We 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.

## Credits

This package was created by [Loan Vulliard](http://vulliard.loan) @ [Menche lab](https://menchelab.com/).  

BioProfiling.jl relies on several amazing open-source Julia packages, listed in the requirement file (see [*Project.toml*](Project.toml)).  

If 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:

    BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations

    Loan Vulliard, Joel Hancock, Anton Kamnev, Christopher W Fell, Joana Ferreira da Silva, Joanna I Loizou, Vanja Nagy, Loïc Dupré, Jörg Menche

    Bioinformatics 2022; 38: 1692–9. DOI: https://doi.org/10.1093/bioinformatics/btab853

We 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.