Package for cell (morphological) profiling

Hi there.

I am currently working on a package compiling useful tools and structures for handling morphological profiles:

Concretely, part of my research work involves High Content Screens in which we measure many parameters to describe cells in different conditions (e.g. treated with specific drugs). This can be done in many ways but you always end up with large matrices (typically one row per cell, one column per measurement or metadata field) that you need to filter and normalize before comparing these profiles between them. Most of these steps are conceptually similar for all such analyses and I ended up creating a framework that I find helpful and would like to share in the form of a package.

I already assembled a few features and there is still quite some work needed, especially in improving the documentation. I read the Pkg documentation about creating packages and the style guide but I still only have vague ideas about writing good tests and best practice for dependencies. Any pointer/help on how to do things properly would be great!

I was wondering as well whether it would make sense to migrate this project to the BioJulia organization? There is no real connection so far but the potential user base might overlap.

The working title of the project is RMP for Robust Morphological Profiling but this name is not so explicit and I would consider switching to something else (BioProfiling maybe?) before registering it. Any strong opinion about it?

Of course, if anyone is interested in contributing or applying it and need guidance, please let me know!
Cheers.

1 Like

My advice would be to use PkgTemplates.jl to generate a skeleton. You can the either copy your code over to the skeleton, or mimic the skeleton in your current repo (depending on whether you care about git history or not).

There’s almost no downside to this - a lot of packages are put together under orgs that have a thematic relationship. Biggest limitation is that @Ward9250 and @bicycle1885 are super busy and so things that happen at Org level sometimes fall through the cracks. Incidentally Ben and Kenta - I’d be willing to take some of that on.

Yeah, acronyms like this are generally frowned on for registered packages, but I think MorphologicalProfiling.jl has a nice ring to it.

1 Like

@koalive if you want to rename and move it to BioJulia let me know, and I’ll send you an invite.
@kevbonham I’ll review your permissions in the morning, so you have access to do more things like this.

Thanks @kevbonham for the tip.
@Ward9250 that would be great. I just found out that there’s a lot of information in your contribution guide about how the BioJulia projects are structured so I’ll look into that to organize my repository!