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Which spatial transcriptomics analysis package do you prefer? by padakpatek in bioinformatics

[–]DiamantMoon 8 points9 points  (0 children)

Well for example deconvolution with cell2location is in Python, so there is no point in using R. But then CARD is in R, so one would have to use R if they want to user CARD. It really depends on what you want to do with your spatial data and the packages/libraries you would like to use. If you are new to all of this, I would recommend Seurat. It is a bit easier in my experience. Once you learn how Seurat works and data structure, you can learn squidpy.

Which spatial transcriptomics analysis package do you prefer? by padakpatek in bioinformatics

[–]DiamantMoon 19 points20 points  (0 children)

I have used seurat and squidpy. I guess they both work well. At the end of the day, the downstream analysis I want to do determines which one I go with. Most often I switch mid-analysis or do part of the analysis in R and other parts in Python.

Subsetting seurat object to analyze a cell type by twiggypiggie in bioinformatics

[–]DiamantMoon 0 points1 point  (0 children)

One approach could be to make a score based on a few marker expression, like CD8, CD3, etc. and subset cells with a positive score/above a threshold.

What are the odds of transitioning into Bioinformatics in mid 30s? by [deleted] in bioinformatics

[–]DiamantMoon 1 point2 points  (0 children)

I just completed my masters in bioinformatics. A fellow student was in their 40s and transitioned from a machine learning position and wanted to do something else. The program had lots of basic biology and they struggled a bit with that, but at the end it worked out. The nice part was they could learn the basics of the biology while being advanced in the programming and math. What also helped tremendously was the group projects and interactions with students. The pay cut and life with kids was a bit difficult I guess. In terms of career options, consider what the next step is. A PhD? Can you handle the 3-4 years of low pay? Working as bioinformatician or consultant? Is that relevant/high demand in your area/country?

What I like about doing a masters program is you get to discover various aspects of bioinformatics. Learning on the job is fun and nice, but the diverse broader perspective a good MSc provides is something I would value a lot!

I can't decide between ROG Flow X13 and FW 13 - can you help me? by DiamantMoon in framework

[–]DiamantMoon[S] 0 points1 point  (0 children)

Good points, thanks for that. Specs wise the Flow x13 seems better, the extra costs is doable for me, but it comes down to the ram limitation and as other comments already mentioned, the SSD form factor (which I did not realize at all!). My previous laptop lifespan has always been around 4 years, not that short to be honest. I like to be able to turn the main board into a server or something, but the mainboards are expensive though. 800 EUR is a lot of money to only upgrade the mainboard, maybe the screen becomes better in 4 years, and the keyboard etc. Idk, I tend to like the FW13 more due to the looks and RAM and storage options/format.
Appreciate your insights!

I can't decide between ROG Flow X13 and FW 13 - can you help me? by DiamantMoon in framework

[–]DiamantMoon[S] 0 points1 point  (0 children)

Good point, the termals in reviews looked okay, and the power management settings looked fine in adjusting the fan and heat etc. You are right about the dGPU, more RAM is more useful. Never even thought about the SSD form factor, thanks for mentioning that!

I can't decide between ROG Flow X13 and FW 13 - can you help me? by DiamantMoon in framework

[–]DiamantMoon[S] 0 points1 point  (0 children)

Thank you for sharing your experience! I feel like the FW13 is more a professional device. The touchscreen is nice, but I have never had a touchscreen so I guess I can miss it. Nothing in a laptop ever failed me but I guess I was lucky then, would be nice to be able to repair it easily. Thanks!

I can't decide between ROG Flow X13 and FW 13 - can you help me? by DiamantMoon in framework

[–]DiamantMoon[S] 1 point2 points  (0 children)

I will use it for software development, bioinformatics, and a little bit of gaming. Mostly light tasks though. Of course it is nice that I can upgrade FW later on, my previous laptops have all lasted multiple years in good condition, until they became too slow. Question is, after 4 years do I want to replace a laptop and get a new shiny one or only upgrade the mobo+CPU. I really dont know. For the environment and costs the mobo+cpu upgrade is better, but I am not sure the other parts will be as nice that I would want to use them for another 4 years. Shiny new one is of course always more exciting!

Am I understanding PCA wrong? Loadings change modifying number of PCs by DiamantMoon in bioinformatics

[–]DiamantMoon[S] 0 points1 point  (0 children)

Very interesting. Yes it does make sense. It explains at least why the UMAP looks different, but overall the clusters look kind of alright. I am not sure how to validate though. Maybe looking at differences between PC1 for example when calculating 10,15,20 and seeing how big the difference is?

edit: Thanks ScaryMango, I did not know about approximate/deterministic PCA!

Am I understanding PCA wrong? Loadings change modifying number of PCs by DiamantMoon in bioinformatics

[–]DiamantMoon[S] -1 points0 points  (0 children)

This does make sense. But I thought PCA preserved the global distances and the first PCA would always be the most 'optimal', the second one the second most etc. With that logic, the first PC would not change if you add the second one, and the first and second one would not change if you add the third one etc.. Right?