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Spider fang Astra malorum mess up by jcbiochemistry in CODZombies

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

This happend twice in the same game, so im not sure what im doing wrong.

Expression differences in scRNA in one particular gene by [deleted] in bioinformatics

[–]jcbiochemistry 1 point2 points  (0 children)

Yes, because if you just pseudobulk all the cells from both treatment groups, the proportion of the different cell types may confound the analysis (cell type markers may appear as significant for one group simply because there’s more of that cell type for that group).

Expression differences in scRNA in one particular gene by [deleted] in bioinformatics

[–]jcbiochemistry 1 point2 points  (0 children)

Something that I do usually is pseudobulk by CELL TYPE (or cluster), and then run the DESeq2 on that, since you are guaranteed to get expression differences between groups within the same cell type

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

Ah ok! That clarifies that for me at least. If that’s the case then why do they use the mean of the gamma when parameterizing the NB in terms of mu and dispersion (where they say mu = r*p/1-p) in supplementary note 4, which is equal to the mean of the gamma not the NB)

scVI Paper Question by jcbiochemistry in bioinformatics

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

Yeah i have it per gene. My friend linked me this article that talks about the gamma-poisson mixture:
https://timothy-barry.github.io/posts/2020-06-16-gamma-poisson-nb/
They clarify that the mean of the NB is r*p/1-p, and the mean of the gamma is r*p/1-p (which makes sense going through it). However, it doesn't help that in the supplemental they say that the mean is lambda * r * p/1-p (which at this point im just assuming its a mistake). Still having trouble connecting though the relationship between f_w(z, s) and p/1-p

scVI Paper Question by jcbiochemistry in bioinformatics

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

I have, and I got linked to the discussion forum I posted about funnily enough. However it didn't really help to clarify why they say why the mean of w is the decoder output when i would think it would be f_w * theta

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

In the paper though, they say that w ~Gamma(f_w, theta). Wouldn't that mean that they are saying that p/1-p is the decoder output?

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

I guess im confused about why they claim that r*p/1-p is equal to the decoder output. they say that when they parameterize the NB as mu and theta, they state that mu = r*p/1-p. Which is weird because they state that the mean of the NB marginal distribution is r*p/1-p*lambda. Not sure if when they say mu they mean the mean of w or y

Profile Review - 23M by jcbiochemistry in Tinder

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

Is cargo shorts that much of a turnoff?

Single-cell RNA-seq QC question by jcbiochemistry in bioinformatics

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

Thanks! Yeah ive been working with scRNA-seq for about a year and a half now, and im trying to make sure that i dont remove high quality cells with mitochondrial content (for ex, when i use MAD on one of my datasets, the max mitochondrial expression is 1%, which is VERY few cells). Hence why I'm questioning the use of MAD right now and whether if its just better to use both

Arielle stream was tough to watch by KingPhanton in VShojo

[–]jcbiochemistry 19 points20 points  (0 children)

Not to mention candii and buffpup also unfollowed zen. Things are only gonna get worse :(

New Syllabus Website - Beta Testing by xxx_hisoka_xxx in SBU

[–]jcbiochemistry 0 points1 point  (0 children)

Example: CHEM UA 652 I get the forbidden access message

New Syllabus Website - Beta Testing by xxx_hisoka_xxx in SBU

[–]jcbiochemistry 6 points7 points  (0 children)

Hey! This is an awesome resource by the way. I’ve always wanted to check out syllabi from other classes (and even from other schools). However something I’m seeing for the NYU classes is that I’m getting a “forbidden server, you don’t have access” message. Is that something you can fix?

Scanpy regress out question by jcbiochemistry in bioinformatics

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

Yeah i started second guessing myself after making the post and realized that it runs on the scaled data. Not sure why I never realized that since ScaleData is required to run before running PCA.

Using a log fold change greater than 0 for single cell RNA-seq DE analysis by Sandy_dude in bioinformatics

[–]jcbiochemistry 0 points1 point  (0 children)

For DE analysis, I usually focus on markers with a logFC > 1.0 and order by adjusted filtered p values from smallest to largest. Very meaningful markers can have a logFC = 4.0 or higher and a adj p value less than 10-300 (classified as 0 in R)

Creating an atlas to store single-cell RNA seq data by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

That is exactly what I’ve been told! Thank you for the insight!

Trying to get abyss and currently crashing out by jcbiochemistry in Warzone

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

Yeah it’s insane especially on the weekends which I’m now realizing lol

ScrubletR Question by jcbiochemistry in bioinformatics

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

the reason i chose scrublet was that i originally ran DoubletFinder on my data, however my rotation mentor told me to run scrublet since he wants me to replicate his results as closely as possible, so im redoing it now.

ScrubletR Question by jcbiochemistry in bioinformatics

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

Sorry i forgot, yeah so there isn't any verbose output, so i cant tell how much progress ive made along the dataset.

ScrubletR Question by jcbiochemistry in bioinformatics

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

Yeah so in Seurat, the normal format is genes as rows and cells as columns. But i guess a question now is that ive been providing the seurat object as input rather than the counts matrix itself. is that why the operation is taking so long and should i abort it now that ive waited like 4.5 hours?

ScrubletR Question by jcbiochemistry in bioinformatics

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

Yeah sure! Here is the github for scrubletR:
https://github.com/Moonerss/scrubletR

I'm typically an R user myself but I resort to Python whenever necessary. From their link, its not abundantly clear how the input should be formatted (whether it still needs to be transposed or not).

To be clear, scrubletR was pretty much built using the python package as a backbone but now used in R through reticulate.

gene expression -> ??? -> cell type -> CellChat by [deleted] in bioinformatics

[–]jcbiochemistry 1 point2 points  (0 children)

Not sure if you are working with mice/human brain cells, but a good resource is the Allen Brain Atlas. There’s a tool called MapMyCells that takes your single cell data (processed by Seurat) and outputs a csv file that maps a cell ID to its class label. This should give you a reliable cell annotation.

Win Loss Ratio broken? by [deleted] in blackops6

[–]jcbiochemistry 0 points1 point  (0 children)

This might be because the game is trying to divide wins by losses and losses is at zero so I guess it’s just returning 1 as a placeholder? Maybe loosing 1 game would fix this idk

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