method_CCST

[naveedishaque]

Update metadata: https://docs.google.com/spreadsheets/d/1QCeAF4yQG4bhZSGPQwwVBj_XF7ADY_2mK5xivAIfHsc/edit#gid=0

Details of method (publication, GitHub): https://www.nature.com/articles/s43588-022-00266-5 https://github.com/xiaoyeye/CCST

[Jieran-S]

Hey @theinvisibleliya are you still working on the method? If you are, would you think it's possible to finish the implementation before next Monday? Otherwise, I can help you with your progress and finish the implementation. :)) Let me know which way you prefer! Thanks!

[theinvisibleliya]

Hey @Jieran-S , sorry for the delay, I was sick for some time and that shifted my projects for quite some time... I would love to finish it actually:) How about I do some work on it tomorrow and then contact you if I need help?

May I ask you why do you have a specific deadline? Are you going to present a method overview some time soon?

[Jieran-S]

Good to know! take your time to finish it --- doesn't have to be tomorrow but if you need any help just let me know!

We're indeed thinking about an overview sometime soon. We hope to generate some results and some overview of the current status and present them at the town hall in mid to late Feb (mentioned in Slack too) so we're updating the remaining methods in the Google sheet. We're mainly checking in if the authors are still working on the implementation. If you need more time, just do it and initiate the PR once it's done. :))

[theinvisibleliya]

@Jieran-S Hi Jieran, I will work on CCST today, sorry for the delay. I will keep you updated:)

[theinvisibleliya]

@Jieran-S Okay, I think I need help with CCST. Since it is not an importable package, but a command-line tool, I encountered a couple of problems. So far, I managed to clone their repo into a temporary directory, solve all the dependency issues and get it to run with their default/tutorial data. But I didn't manage to get our data into the form which they require...

I firstly tried running it without preprocessing, but it did not work. Now I am trying to integrate their preprocessing as well, but had no luck with getting our data into their requirements so far.

There is another thing: in the description, they say that CCST works on both, single-cell "sc" and non-single-cell "nsc" data. However, for single-cell, their code is very specialised for MerFISH data... they write that it can work on other datasets, but there is no proof to that.

Moreover, they have a couple of hardcoded file names in the code... It is a challenge to connect all the dots and rename files so they fit to their required ones. During the hackathon, I talked to a couple of people from my team, and they all advised me to take their repo "as-is", clone it and use their scripts, but since I encountered so many obstacles, I was thinking that forking their repo may be a better idea...

Other observation: Their GitHub code has nearly no commit messages except for "Added files via upload" and there are some outstanding code issues, which were not answered in the last 9 months. The author seems to be active on GitHub, but this repository was not updated for a long time.

I cleaned up stuff which did not work, but left the cloning into the temporary repository and dependencies in my code. This should be helpful.

@Jieran-S, do you want to take a look at their repo and talk about it? I could totally use your opinion and help implementing this method. You are also welcome to play around on "method_CCST_liya" branch and change anything you want :)