search

HelenaLC / BiocSpatialChallenges

1 stars 1 forks source link

SpatialDE Challenge #1

Open davidecrs opened 3 years ago

davidecrs commented 3 years ago

Hello @HelenaLC @drighelli @lmweber,

I attended the Bird of a feather of the current EuroBioc2020 regarding the “infrastructure to enable spatially resolved transcriptomics data analysis with Bioconductor”. I have read the proposed challenges and I would like to contribute to the SpatialDE challenge. I do not have any experience with reticulate or basilisk, yet I’m really interested to this particular challenge and in learning the most suitable tool for this task. Let me know what do you think, I’m open to any suggestion regarding the research plan to follow.

Greetings Davide

lmweber commented 3 years ago

Thanks @davidecrs ! I would suggest trying out Basilisk to begin with, since I have heard very good things about it. However I don't have any experience with it yet either, so please let us know how it goes!

davidecrs commented 3 years ago

Perfect, thanks for the advice @lmweber. So I'll start with Basilisk and I will keep you updated on developments!

milanmlft commented 3 years ago

Hi @davidecrs, I'm also interested in contributing to this challenge. Have you already started work in a repo somewhere?

Regarding the discussion "basilisk or reticulate": I'm still learning how to use basilisk as well, but from what I understand it's not a question of whether to us either basilisk or reticulate, but rather to use them both. Reticulate lets you call Python from within R and basilisk makes sure the Python environment and modules stay consistent.

The velociraptor package might be a good example of how to wrap existing Python tools for BioC.

Let me know if I can help out with anything!

davidecrs commented 3 years ago

Hi @milanmlft ,

I think is a great idea to collaborate! I've just finished to build the initial structure of the repo https://github.com/sales-lab/spatialDEr . Now I'm going to start to explore the original python SpatialDE and try it. I will let you know about any other future update.

milanmlft commented 3 years ago

Hi all, just wanted to let you know that spatialDE has been accepted on Bioconductor: https://bioconductor.org/packages/spatialDE/

Thanks for initiating this great challenge!

drighelli commented 3 years ago

Grants @milanmlft and @davidecrs