A flexible Julia toolkit for high-dimensional cellular profiles
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 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
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:
- Have a look at the documentation
- Run our example analysis notebooks
- Check out the JuliaCon 2021 poster presenting BioProfiling.jl
- Read our article published in Bioinformatics
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.