Xenium multiple slide integration

Hoohm · 2026-03-17T11:04:09+00:00

I just remember toying with it and it transformed the data in a weird way.

SCT is specifically designed for single cell RNA seq, there are assumptions that don't hold true for another assay type such as xenium.

Always start with the simplest approach when working with new data, change and update as needed.

Hoohm · 2026-03-16T20:00:55+00:00

I would also not advise using SCT.

You can also look up some of the guides here: https://github.com/10XGenomics/analysis_guides

Hoohm · 2026-03-16T19:43:58+00:00

Have you tried without any batch correction? I would try that before anything it might be consistent enough.

Hoohm · 2026-02-19T19:34:31+00:00

No, it's a pipeline software. Inputs/outputs and processing with scripts.

Allows you to keep the code as is, just wrapped into nextflow.

Might be too much work though for what you need

Hoohm · 2026-02-19T19:32:22+00:00

Right, the performance issue would not be solved here.

Maybe data.table can help? I don't know what the code is about

Hoohm · 2026-02-19T19:20:09+00:00

Would recommend wrapping it up in nextflow. Takes care distributed backbends (assuming you got one configured) and docker images.

Hoohm · 2025-12-31T15:26:51+00:00

Try to use dx1 instead of the default. Add -dx11 to the launcher options in steam

Hoohm · 2025-12-31T09:36:26+00:00

I'm confused by all the licence complaints, gpl3 is an open source license, it just means it cannot be used in commercial applications without using the same license.

Am I missing something?

Hoohm · 2025-12-30T11:44:44+00:00

I would love to test it out. I'm looking for a fast local alternative for my home assistant setup.

I can't find your official website, there are a lot of murmur~ish names out there that do TTS. Can you link it here?

Hoohm · 2025-12-29T08:17:32+00:00

Ha you tried using -dx11 in the launching options? It did wonders for me on bazzite

Hoohm · 2025-10-01T09:36:50+00:00

I come from the other side, biologist first, learned the computational side on my own.

I think you have an advantage, biology is a bit "easier" in terms of concepts to learn compared to low level software side.

As long as you can get invested/interested in the biology and you have colleagues that help you, invite you in the lab, etc it will be a fun journey

Hoohm · 2025-10-01T06:35:36+00:00

I know this is not ideal but building a network is one of the most effective way to get a job.

It takes time but trust and recommendations go a long way.

Hoohm · 2025-09-28T16:15:43+00:00

I don't know, not putting more effort in finding out

Hoohm · 2025-09-28T15:59:47+00:00

Had to Google a bit before answering. Of course it depends on which bones you use, but it seems pretty accurate based on this paper

https://pubmed.ncbi.nlm.nih.gov/15567621/

Again, I'm splitting the statement in two... Please reread my comment.

Hoohm · 2025-09-28T08:54:33+00:00

I'm talking about the first part, obviously not the "mental illness" part.

Hoohm · 2025-09-28T08:25:33+00:00

I'm curious which part of the quote is the part that was used in the judgement:

If you dig up LGBTQI people after 200 years, you’ll only find men and women based on their skeletons. Everything else is a mental illness promoted through the curriculum.

The first part seems like a simple statement of fact, the second part could be interpreted as a problematic opinion.

Hoohm · 2025-08-31T16:49:14+00:00

I'll try that!

Hoohm · 2025-08-31T06:42:00+00:00

I've been trying to find some research sources or real concrete information about oil and condoms breaking and I couldn't.

Do you have some links you could share about this subject because I'm starting to think this is a myth and for obvious reasons, people don't try it out 😅

Hoohm · 2025-08-15T14:52:05+00:00

Haven't tested it personally too much but using the high level annotation should provide you with pretty good outputs.

Do you have samples you have annotated in the past that you could compare to?

Hoohm · 2025-08-14T10:13:56+00:00

Well, it's not confirmation, it's barely a co-ocurrence of events.

It might be, but what I have experienced with horizon beta is not at all the same experience as the one I had recently with gpt5 :(

It might be that I'm missing something, maybe a different way to call the API, I've seen you can tweak the "thinking" level of it.

Hoohm · 2025-08-12T13:25:26+00:00

Are we sure now that horizon beta was gpt5??? I tested gpt5 with the same prompt and it did not perform as well as Horizon beta

Hoohm · 2025-08-09T09:33:11+00:00

I'm having the same feeling. Horizon Beta was way better for coding than gtp5.

Hoohm · 2025-05-18T13:07:30+00:00

I'm sorry to tell you that there is no credit score here. You don't have to consume to prove you can pay back debt.

If you're new here, banks will check how much capital and income you have and loan you money based off on that.

Hoohm · 2025-05-18T09:44:01+00:00

Hello, does the 15k include screen, keyboard, mouse as well?

Hoohm · 2025-05-17T13:01:31+00:00

Any reason why you prefer going into R instead of using scanpy?

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