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BioProfiling.jl

Project Status: Active – The project has reached a stable, usable state and is being actively developed. CI CI codecov Contributor Covenant

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:

import Pkg
Pkg.add("BioProfiling")
using BioProfiling

Local installation

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

import Pkg
Pkg.activate(<pathToThisFolder>)
using BioProfiling
Pkg.activate()

Installation from GitHub

Use the following to install the package:

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

You can then import the package normally:

using BioProfiling

Learn more

Contribute

We welcome all sorts of contributions to this project! See our contribution guidelines and our code of conduct for more information.

Credits

This package was created by Loan Vulliard @ Menche lab.
BioProfiling.jl relies on several amazing open-source Julia packages, listed in the requirement file (see Project.toml).
If you use this tool in your research work, please cite the article 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, their biological interpretation as well as the package in itself.