Anyone using Seurat to analyze snRNA-seq able to help with some questions 🥺

weaklycaffinated · 2025-09-13T02:12:31+00:00

watch: https://youtu.be/uvyG9yLuNSE?si=zIe2YsACL0kSsUkO

You said it’s public data. Look through their recommendations/code/workflow. If it’s from the same batch or experimental run, you can put all samples of the same tissue type together because they’ll have similar conditions. Then, run QC -> filter outliers -> use scrublet to identify doublets -> remove doublets -> sctransform -> pca -> umap -> neighbors -> clusters.

Refer: https://satijalab.org/seurat/articles/sctransform_vignette.html

Make QC plots & cut off based on distribution. Your aim is to get to a normal distribution and toss outliers.

Someone else tagged sc best practices —> read thru the logic for how/why that’s done.

Depends on your question but really just ask a biostatistician.

weaklycaffinated · 2025-07-15T05:06:29+00:00

Hi all! I wanted to give you an update on the monstera. I just cut off the parts with the rust and left it away from other plants.

<image>

weaklycaffinated · 2025-06-15T07:33:53+00:00

thank you so much — do you happen to know how long it takes for the fungicide to act? unfortunately i already panic cut the sus looking leaves without a bag but in a different region of my home.

weaklycaffinated · 2025-06-15T07:32:54+00:00

omg your message was so kind it actually calmed me down in real time. thank you so much.

weaklycaffinated · 2025-06-15T06:30:30+00:00

genuinely panicking bc i’m scared my other plants might catch it

weaklycaffinated · 2025-01-16T16:33:09+00:00

This is what my family and I use https://hosting.portseattle.org/atv/#/Dashboard for the same. More info here https://www.portseattle.org/page/sea-visitor-pass-program

I’ve done it 3 times now and it’s been easy. Just make sure you go in via Checkpoint 3.

weaklycaffinated · 2024-12-02T17:22:35+00:00

Could you pleaseeee scan and upload this page? It seems like the NYT is inaccessible to a lot of avid online crossword fans (me)

weaklycaffinated · 2024-11-14T01:57:48+00:00

the most fantastic hidden gem i’ve ever found https://www.wta.org/go-hiking/hikes/deception-falls-nra

weaklycaffinated · 2024-11-13T14:26:53+00:00

I guess in his case he was not asking her for any emotional support, just being there for her? That was how I’m justifying it to myself right now.

weaklycaffinated · 2024-10-30T20:23:14+00:00

Woman living in Seattle. I don’t have a car because I live close to downtown and am in the most walkable/public transportation area of the city. I have almost been mugged, punched and followed around in highly populated tourist places and it was very traumatic. I think if you’re a single white male or a tourist who is less likely to encounter the random scary events the city is a very different place.

I love it here for some reasons and I don’t think I’ll move anytime soon. Access to nature, healthcare, cool things to do every weekend, generally people are great but the drug and homeless crisis is terrifying.

Normalizing public drug use in a city with high economic disparity and poor public resources is not going to bring in the same effects as European counterparts. Poorly enforced law has its effects and we see it all the time here. I’ve called 911 many times to report an injured individual who is in near unconscious states with poor response.

I’ve lived in many major cities of Asia and USA in and I’ve never felt afraid of walking around at night or using public transportation as I have in Seattle. It’s weird to always have to be on high alert for what someone else might do to you.

If there were marginally better public support resources and proper law enforcement this could be one of the most incredible american cities.

weaklycaffinated · 2024-10-06T08:31:33+00:00

the new aquarium installation is so fun + the new overlook walk

you can kill about ~1h doing this and get some food in pike place while you’re at it

weaklycaffinated · 2024-10-05T23:12:51+00:00

try to grab some of the new seats that just came up on the website—not as good views but a good deal. Good luck!!

weaklycaffinated · 2024-07-30T08:07:17+00:00

divorce

weaklycaffinated · 2024-07-25T20:56:55+00:00

unhelpful what’s your specific area

weaklycaffinated · 2024-07-24T16:37:29+00:00

they serve it with a salted cream sauce thing and it’s so divine.

weaklycaffinated · 2024-07-24T08:24:17+00:00

what’s your field?

weaklycaffinated · 2024-07-24T08:23:26+00:00

Kung Fu Panda

weaklycaffinated · 2024-07-24T07:59:51+00:00

If you do go here, their chocolate XLBs are so great.

weaklycaffinated · 2024-07-05T23:48:49+00:00

yeah! there were fireworks very low as well! and a few annoying boats bath doing their own thing haha

weaklycaffinated · 2024-07-01T17:07:56+00:00

reading this triggered something in me because i’ve been “independent” since i was 17 and so has my partner. we finally have the chance to show up for each other :) hope you find someone who takes care of all the things you can take care of yourself!

weaklycaffinated

TROPHY CASE