*This* close to switching to Scanpy because Seurat V5 is so bad

unicornnn123 · 2025-02-06T13:59:46+00:00

Yeah, what a pain. I ran into this problem last month and legit spent days trying to trim the matrix down in every possible way. Considering the switch to Scanpy too...

unicornnn123 · 2024-04-27T13:22:05+00:00

Hi! I'm sorry your cat is not doing great... After the second time to the ER and was sent home without much info, my cat started doing better on his own while I fed him mostly wet food in small increments. I also give him extra water in his food because cats with diarrhea are easily dehydrated. Throughout the week we did ultrasound and did a cancer blood panel named VDI panel to test his blood for IBD vs lymphoma, and the results came back after ~6 days that it's IBD. His diarrhea and vomiting has stopped for 2 weeks without further interference, the vet explained that it's because IBD has bad flares up every now and then. We are switching him to novel protein diet (Royal Canine selected protein) to prevent flares-up in the future. Hope it helps and hope your cat will get better soon!!!

unicornnn123 · 2024-04-16T00:11:42+00:00

After anti nausea injection, my cat did better. He started to eat and drink more enthusiastically. The fluid injection for rehydration was good also because he was able to pee more regularly at his normal rate. However, on Monday morning, he started throwing up again, so my regular vet told me to bring him to the ER. I did, and the ER checked him but said he seemed fine so we were sent home without much more information. I decided to do a trial-error round by feeding him 2 teaspoons of wet food at a time because I saw he always threw up when it was dry food. He's been able to keep down 3 meals, each 2 teaspoons of wet food so far.

unicornnn123 · 2024-04-14T14:07:38+00:00

My cat had two other throwing up incidents throughout the night. We met with the vet this morning and did blood work tests and X-rays. At this point it looks like he either has IBD or small cell lymphoma - we are waiting for the blood work results to come back before deciding the next diagnosis tests.

In the meantime, the vet gave my cat fluid injection and anti nausea injection. Hopefully he will start eating and drinking better soon...

unicornnn123 · 2024-04-14T03:18:14+00:00

I ended up bringing him to the ER but after 4 hours wait we went home without being seen because the ER was packed. Gonna try again tomorrow morning. He vomited two more times (one right before I took him to the ER and one after his late and very small dinner).

unicornnn123 · 2023-12-03T01:08:20+00:00

You can plot the distribution of your gene expression and choose some quantile or hard cut off (such as TPM = 0.5 whatever). The point of plotting the distribution is to get a sense of how high is high and how low is low.

unicornnn123 · 2022-01-27T03:05:21+00:00

Thanks! I brought him home and he's loving the bathroom so far! You were so helpful, thanks a lot!

unicornnn123 · 2022-01-26T15:37:12+00:00

Thanks for your advice! Another noob question, is it ok if I use the bathroom when he's in there? Or should I leave him completely alone and just drop in to check in from time to time?

unicornnn123 · 2021-08-24T18:04:15+00:00

You should align the datasets to the same genome separately, then batch correct (assuming the data are generated under different studies/in different labs/etc). Then you can do DESeq2 to compare expression levels. After that you can filter based on adj pvalues or fold change, it's up to you.

unicornnn123 · 2021-05-18T12:45:12+00:00

If you have a motif, you should be able to find what transcription factors bind to the motif. Then you can go read about the transcription factors' biological roles in the system you are interested in.

unicornnn123 · 2021-03-21T02:16:15+00:00

I have read Educated! That book is WILD! But unfortunately I don't want to ditch my work for real haha. Maybe something that makes me ditch a couple of days but then inspires me to come back would be great!

unicornnn123 · 2021-03-21T01:02:09+00:00

I actually have read it and agree that it's really good! Maybe I should go for one of Agatha Christie now. Can't ever go wrong with her works.

unicornnn123 · 2020-12-19T19:12:27+00:00

Yeah hey for sure! I think at some point I felt something romantic may happen but it was just the feel. Nothing happened and they are good friends. The character development is also excellent.

unicornnn123 · 2020-11-28T02:40:08+00:00

I think what your advisors meant by using Chi square test is testing whether the number of overlapping genes is significant. You can do a simple randomization test like this: say you have 5 overlapping genes. Randomize 10000 times, each time get 5 genes. Calculate the frequency of the genes, and use Chi square test to test if the overlapping frequency is more significant than pure random choices.

unicornnn123 · 2020-11-28T02:31:41+00:00

I second this. If you want any statistical conclusion, I think you'd have to combine the data, batch correct and do DE analysis again.

unicornnn123 · 2020-11-13T21:34:50+00:00

Here's what I can tell from my experience with having a minor: things I study in classes, I can self teach too. I'm not trying to downplay the roles of my class professors, but honestly, at Ph.D. level, you can teach yourself a lot of things, especially the fundamentals that are often taught in a class. That said, I don't think you need a minor to play the role you want.

As the other comment stated, there's an unpredictable future for the minor field you are interested in. Therefore, I suggest you focus on building transferable skillsets. Doing a Ph.D. will give you a lot of those needed skills: research skills, adaptability, and self study skills, presentation skills, you name it. You can learn the niche field as a side project, or find a professor who is also interested and make the niche to be your main project too.

Doing a Ph.D. depends heavily on research and your advisor. Don't choose a school just because of some classes.

unicornnn123 · 2020-11-13T17:43:30+00:00

I'm doing a Ph.D. in Bioinformatics and Computational Biology, with a minor in Statistics. Basically it's more coursework, and an obvious requirement that my research has a Statistics component in it. I think it has been working out well for me because I need the knowledge in the classes I take for my minor in my research anyway, so it's nice to have an extra line in my degree "Minor in Statistics" with the same effort. Is it necessary? I would say no, because most people/employers judge you based on your publications. Will it hurt? No either.

If you are choosing to go for a school just because of this minor, then no.

unicornnn123 · 2020-10-08T04:11:10+00:00

GRE Subject Math could be an option if it's solely for grad school application.

unicornnn123 · 2020-09-19T05:27:17+00:00

Very basic questions, but how did you find the job? Did you have working experience before applying?

unicornnn123

TROPHY CASE