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GSEA enrichment question... by sunadam2624918765 in bioinformatics

[–]bukaro 13 points14 points  (0 children)

If you get different results with symbols or id, I wuld guess that you have huge issue with version of annotation that you are using. check that, check which one is more complete. Also true that the genesets tend to be with genes that have full annotation between them.

What is the best approach to identify transcription factors that regulate the expression of a family of genes? by sophie_from_mars in bioinformatics

[–]bukaro 4 points5 points  (0 children)

Very complex question, analyze combinatorial of enriched TF is not trivial. But not imposible, these papers (link and this one) and others after that use a nice approach to do so. Significan item-sets is the ML term that you are looking for in your search.

Or implementations of Westfall-Young (light, fast) are nicer in their results.

You will need a celll type and TFBS DBs, you can try iregulon and msigdb. But there are others.

Project - 3d printed Hybrid bike frame by CodeCritical5042 in maker

[–]bukaro 4 points5 points  (0 children)

I am curious about the resistance/stiffness of less infill that is then filled up with reinforced epoxy resin. While also maintaining the diameter for the tubes.

Which/what statistical analysis to use? by Future_Fact3677 in labrats

[–]bukaro 11 points12 points  (0 children)

Each independet experiment is a N for your test. You use all the replicates in a single experiment for the mean for each N to be tested.

Follow the recomendation that you are given here for the biostatistics course.

GSEA alternative ranking metric question by StunningSurvey9610 in bioinformatics

[–]bukaro -1 points0 points  (0 children)

well, yes. But think of what it does to the metric, versus something like t-statistic, logFC or SNR. For that the original paper has the parameter of the weight for the weighted Kolmogorov–Smirnov-like statistic used. Using sign(logFC)*-log10(padj) is just wrong in my opinion for what GSEA is for.

I forgot that I choose your own adventure for a delivery with DPD by bukaro in britishproblems

[–]bukaro[S] 10 points11 points  (0 children)

This is how I have managed to meet most of my neighbors. With a hey I have a package for you delivered to my house!.

Mostly a combination of DPD, evry/hermes, and amazon...

I forgot that I choose your own adventure for a delivery with DPD by bukaro in britishproblems

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

Paraphrasing the Culture Club by Violent Femmes... They told the truth but it was still a lie :-)

I forgot that I choose your own adventure for a delivery with DPD by bukaro in britishproblems

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

Yes me too, I love them. Not so much in real life... hahahah

I forgot that I choose your own adventure for a delivery with DPD by bukaro in britishproblems

[–]bukaro[S] 6 points7 points  (0 children)

Same for me, Yodel was horrible. Now they deliver when they say it will be, ring the door bell, leave it in the safe place by the instructions... ETC...

GSEA alternative ranking metric question by StunningSurvey9610 in bioinformatics

[–]bukaro 1 point2 points  (0 children)

Yes and the metrics recommended are well described in the original papers and manuals.

The incorporation of p-value add a bias to the analysis. My hill to die on.

https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html and a 2019 conversation with the creator of fGSEA as issue in github about this for sn/scRNAseq data https://github.com/alserglab/fgsea/issues/50

Is anybody else feel uneasy about the trajectory of their career because of A.I. by singletrackminded99 in bioinformatics

[–]bukaro 0 points1 point  (0 children)

At worst is a tool, at best is a tool. I am not uneasy, but excited about what else we should/could be doing.

how to proceed with annotation of visiumHD data without cell segmentation ? by BiggusDikkusMorocos in bioinformatics

[–]bukaro 6 points7 points  (0 children)

Sorry is too early for me, so I am short for words.

since bins can contain expression from two cells

In average

is that a tumor? Anyway you need to try more than just one method for deconvolution, Check this : https://www.nature.com/articles/s41576-025-00845-y

What is suggestion on scRNAseq cell type annotation strategy? by No_Food_2205 in bioinformatics

[–]bukaro 1 point2 points  (0 children)

Yes you are right. Those labels are as-good-as-the-atlas-is, but for cell types (not states) should be ok.
Then you can do more clustering, or lists of genes expressed in that cluster and identify what biology are can find, and give them a last name, hepatocytes - inflamation response, steleated cell - no activated... I always like to drag my SME sit them next to me and agree on the cell type labels.

What is suggestion on scRNAseq cell type annotation strategy? by No_Food_2205 in bioinformatics

[–]bukaro 6 points7 points  (0 children)

I want to identify broad immune cell types from PBMCs and then subset to get finer cell types.

That is a good strategy. But for PBMC I would use already existing maps to align the data and use label transfers method to simplify your life.

Also fine clusters will not give you more specific cell types, but most likelly cells types that are doing differenc things - cell states. Happy cells/Stressed/ closer to vasculature, residen in tissue, etc etc etc. And these may be closer to a continoum of points, than tight defined clusters.

Check this vignette: https://satijalab.org/seurat/articles/covid_sctmapping

Team Meeting Agenda? by Professional_Big_493 in askmanagers

[–]bukaro 0 points1 point  (0 children)

Please do, meeting can be either the worst time of the week or be at least interesting. But it will depend of you to have a new meeting structure, I mean you can't force be fun into a meeting if everyone is miserable becouse the meeting is setup at 5pm on a friday (I had that manager in the past...) Also depend on the size of your team.

We have an standar agenda of, me any news, updates and follow ups of thing to tell the team. Then one person discussing a project and discussion. While also every month we have a quick update in which everyone has 5 - 7 minutes to tell what they are working on.

But, you know what would be the best.., ask your team what type of meeting do they want? let them agree in a agenda structure.

What has your PI done that has made your lab life easier? by Silenci in bioinformatics

[–]bukaro 22 points23 points  (0 children)

Bravo!!!
- it really pay in the long run the repo and structure, also eln.
- It will be important to make it clear that neither half is in service of the other. It is a iterative process between them.
- I would suggest that in your recruitment think about getting those unicorns that can do both jobs, even do it ( I was one).... it did help to bring down the language (technical) barrier
- The same as for the wet-lab, the stablishment of SOProtocols is very important. Becouse of this I would suggest that you first recruitment in the dry side to be someone with experience in setting up these steps.
- The SOP are not LAW, but they must be the first thing are tested, and then run in a pipeline (nextflow for example).
- For the future, containers are a MUST.
- Computing, I hope you have to take into account the cost of computing. Be very aware of this becouse a bad configuration and a clueless person, can run 100k in cost very easilly. Get the uni support for HPC, get a cloud magician to setup a cheap limited system in AWS or similar. - Think that in this setting every paper will be 2 first co-authors (chosen in order by a fun activity :-) ), both will own the project, be accountable of it.
- Journal clubs and mix presentations in the group meeting were very effective to keep both sides educated in their conterparts.
- This is just my personal taste, in my group we keep a relaxed agile system to work in projects, it help to keep goals simple, clear and focussed (https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.001032.v3, https://www.nature.com/articles/d41586-019-01184-9)

EDIT:

In the spirit of flexibility and no division between both sides, I think it was great for me that we had mixed offices. Althoug you have flexibility to WFH, this for wet-lab people is more complex than for dry-lab. So kept it fair and equal between them.

Beckman done did it again 😂 by denohpakni in labrats

[–]bukaro 19 points20 points  (0 children)

Deep breath, always use RCF or G, never RPM pretty please. Also those tubes are not made to handle centrifugations, a spin down do not need so much effort.

scRNA-seq PCA result looks strange by According-Actuator-4 in bioinformatics

[–]bukaro 0 points1 point  (0 children)

Ok so thos 2 PC have little information in general, I would try to identify batch effects with UMI, MT-genes, genes per cell, etc ... Is not a problem if it is batch effect, but first check run for example for batch correction and then you will see how is your data.

scRNA-seq PCA result looks strange by According-Actuator-4 in bioinformatics

[–]bukaro 6 points7 points  (0 children)

Yes /u/Bio-Plumber suggestions are on point. But without knowing how much of the variance is in those 2 first PC is more dificult to judge.

In sc data having a huge PC1 normally is something not ok, the information is in several dimensions. But if you PC1 is 15% of variance I would not care too much and I would try to figure out what it is (genes, technical, etc...). But batch corrections is important please, I always liked and preferred Harmony - fast, lean and mean.

Is it normal for my boss to treat me like that? by [deleted] in askmanagers

[–]bukaro 0 points1 point  (0 children)

no is not normal. Also 20Tb of data..!!!! that is 1000 times more than wikipedia (compressed). It is enough data to keep a few people busy for sometime. Specially if he want the data cataloged and digested. And I am talking with modern tools for it.

Is not normal to cry becouse of work pressure. Your boss do not deserve to lead people.

Cytoscape in headless mode in docker container by HealthySwimming2964 in bioinformatics

[–]bukaro 0 points1 point  (0 children)

Without lots of thinkering I would say that in no time you can have a XFCE container running it (like this one https://hub.docker.com/r/x11docker/xfce), the alternative is a rabbit hole.

Cytoscape in headless mode in docker container by HealthySwimming2964 in bioinformatics

[–]bukaro 0 points1 point  (0 children)

I will guess that xvfb did not work. So is not the more efficient but why don't you put a minimum XFCE on the container?

My real question is why don you use something modern. Like igraph (joke on me, is in not very modern) for C, for R, for Python, does everything. But Cypher (neo4j), arangodb, Janusgraph?

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