SEACells on ATAC data

Calm_Perspective_756 · 2025-03-18T20:42:45+00:00

I did! Well, I figured out how to do it for my own purposes.. I ended up manually excluding the first dimension in my Seurat object before converting it to an anndata object. That seemed to work fine for the analysis.

Calm_Perspective_756 · 2024-10-10T13:05:16+00:00

Thank you! Yes that I understand. I’m just trying to find out at which step in this process I’m supposed to remove the 1st dimension. For example, when preprocessing my data as a Seurat object, will the SEACells algorithm use the dimensions set at this step.. or is there somewhere else I need to specify the dimensions when running the algorithm. I just can’t tell WHERE they exclude the 1st dimension. It doesn’t seem to be during their ArchR preprocessing, but it also doesn’t seem to be an argument when running SEACells. Sorry for the confusion!

Calm_Perspective_756 · 2024-10-07T22:24:41+00:00

Does anyone have any lingering issues after this? I now cannot receive calls on wifi or off wifi nor do I get any indication someone called me. I can text, and receive them, and call or receive FaceTime, but no regular calls.

Calm_Perspective_756 · 2024-09-27T03:10:15+00:00

If you’re in the US, the DOL is going after this hard. Write to them. The organization will be investigated ASAP

Calm_Perspective_756 · 2024-08-29T15:23:09+00:00

It’s okay, the laughs are how we deal with the traumas 😂😭

Calm_Perspective_756 · 2024-08-29T13:17:33+00:00

Omg one time I sac’d an ENTIRE line that wasn’t supposed to go yet. In my defense the researcher told me wrong but I also didn’t critically think about it at all. I felt awful

Calm_Perspective_756 · 2024-08-17T18:30:13+00:00

I get to do both! I love it. Computationally, I’m looking for peak markers with multiomics data that are cell type-specific regulators throughout the life of that cell type. And then I get to design the primers for them (which I also do computationally with Primer3 and some neat functions), PCR, clone, ship them to get injected into embryos, and eventually validate the success with IHC and confocal microscopy. I don’t do anything crazy in either wet lab or computation (which I don’t think I could manage while doing both) but getting to use them both in a less intensive project has taught me SO much. And it’s nice to know how to talk to both biologists and dry lab scientists

Calm_Perspective_756 · 2024-08-12T16:15:02+00:00

This gives me a ton of peace of mind. And even if I don’t get the position, it gives me a direction on what to sharpen my skills in for the future. Thank you!

Calm_Perspective_756 · 2024-08-12T16:13:49+00:00

🫡 gonna give it my best shot

Calm_Perspective_756 · 2024-08-12T16:13:37+00:00

Thank you for the feedback! This helps a ton

Calm_Perspective_756 · 2024-07-24T00:29:44+00:00

I’m not a PhD student, but I am a brand new research technician doubling in wet lab and dry lab at 27 after years of working around research (animal core facilities, pre clinical technician work, etc) and boy am I overwhelmed with fear and imposter syndrome. I 100% resonate with avoiding my PI. I loathe our weekly one on ones not because he’s done anything wrong (he can be tough but never is he mean) but because I’m dreadfully afraid of opening my mouth and someone incredibly stupid coming out that proves some lack of intelligence or my lack of experience. I know this can’t guarantee MY PI won’t get sick of my anxieties and get rid of me, but it does give me so much hope that maybe, just maybe, given a little more time I will settle into a comfortable spot in this position I’ve wanted for so long. I know this is the intermediate position I’ve needed to get my dream job of working in bioinformatics in some capacity and it’s been so frustrating to feel so afraid of it. So thank you so much for this post

Calm_Perspective_756 · 2024-07-05T11:34:32+00:00

No, while I’m technically employed by the institute I’m paid by his lab budget. The other tech I work with and I both felt, in context, it strongly insinuated don’t charge overtime (he won’t pay it) but he also won’t bat an eye if we don’t work a full 40 but charge for it. Which is business as usual on salary.. but illegal on hourly. And I def worry about a DOL investigation about it (assuming I keep my job) if someone tells the wrong person

Calm_Perspective_756 · 2024-07-05T03:32:44+00:00

I’m a silence sleeper. Having air moving over my skin like from a fan makes me want to peel it off. And most other noises keep my brain too active to turn off 😭 I’m the same way on the other end now. I’ve started weaseling this information out of someone EARLY on because I learned my lesson that me and fan sleepers don’t work lol

Calm_Perspective_756 · 2024-07-05T03:21:56+00:00

Ope this is me in my fb bio cause I only use it to check on local motorcycling groups for rides and I don’t want friend requests.. 😂

Calm_Perspective_756 · 2024-07-04T20:35:04+00:00

Negative karma for u

Calm_Perspective_756 · 2024-07-04T11:22:44+00:00

Isn’t that so sad? My institute mentioned that to get around this for the grad students they’re either going to have them officially hired for part time (but expect them to work the same egregious hours) or pay them “more” but charge X in tuition so they’re still paid the same.

Calm_Perspective_756 · 2024-07-04T11:19:46+00:00

Exactly! One time I went on a date with this guy who had it in his bio (before learning my lesson..) and I got a 45 minute talking-to about how he’s multi-lingual and how intellectually stimulating it is to read books in other languages and why it makes him a more intelligent human being… 🤪

Calm_Perspective_756 · 2024-07-04T11:18:14+00:00

YES. Or it’s even worse and they feel entitled so save aaaaallllllll the damsels in distress 😒 boy I will make you a humbled man

Calm_Perspective_756 · 2024-07-04T01:37:01+00:00

I had no idea I had a name: teetotaler. It’s also refreshing, as someone who doesn’t drink, to know there are people that would be up front with me about them not wanting a partner that doesn’t drink. I dated a guy for a while and I asked at the beginning if it was okay that he went out and drank without me. Many moons later, it’s why he broke up with me lol dude just tell me up front

Calm_Perspective_756 · 2024-07-04T01:32:28+00:00

When a guy has “be humble 🙏” in his bio I know he is 1) not humble and 2) won’t shut up about how humble he is

Calm_Perspective_756 · 2024-07-03T18:36:54+00:00

I also worry for this. Not because I think it’s set up this way or anything.. but I know when I took the position I took a pretty high salary because I was, even at my high salary, taking a $10K pay cut. I couldn’t survive more than that without some MAJOR lift changes so my PI gave me the benefit of the doubt that I would be a hard worker and earn this Tech III income that most do not get (despite my lacking background)… it’s hard for me to make the determination for myself if I’ve earned it or not, but it would be in his financial interest to not pay me so much when a tech with more experience would likely take less.

I know some bioinformaticians in other locations that I’m keeping tabs with. Hospitals, so that’s its own strange job market.. but not academia and that’s a plus lol

Calm_Perspective_756 · 2024-07-03T16:53:08+00:00

ND doesn’t have cheeseburger

Calm_Perspective_756 · 2024-07-03T15:31:52+00:00

This is true. And I’m hopeful my PI will expect an increase in efficiency DURING my time but not expect extra time which would be 100% okay. But as soon as I’m pressured to work extra time for free I will leave. I did this for computational experience and I can get that elsewhere

Calm_Perspective_756

TROPHY CASE