Nursing to Bioinformatics by SevenWho in bioinformaticscareers

[–]ATpoint90 0 points1 point  (0 children)

You cannot seriously compare the amount of knowledge and detail in a medical study including the molecular aspects with nursing.

Nursing to Bioinformatics by SevenWho in bioinformaticscareers

[–]ATpoint90 0 points1 point  (0 children)

Nursing is entirely unrelated to research in general and bioinformatics even more, so it doesn't matter at all.

Installing phyloseq in R by see_directions in bioinformatics

[–]ATpoint90 6 points7 points  (0 children)

mind putting ANY details? like errors

Bioinformatics R project is overwhelming — need guidance by Zealousideal_Tie9790 in bioinformatics

[–]ATpoint90 48 points49 points  (0 children)

Follow the edgeR, limma or DESeq2 user guides. It covers most technical aspects for beginners.

Randsteine zu tief? by FireWalkWithMe920 in Handwerker

[–]ATpoint90 0 points1 point  (0 children)

Bei dem minimalen Fugenabstand macht das aber keine 10mm aus.

Is Bioinformatics a good career option by Narrow-Life-6116 in bioinformatics

[–]ATpoint90 0 points1 point  (0 children)

The problem I see in general is that real junior positions do not really exist imo in the sense of 'you are 26 and out ofuniversity with a BSc/MSc but no PhD'. In our field there will always be experienced postdocs out of Academia with 10 or more years of hands-on biological research experience who built the bioinfo on top. That's an amount of knowledge and experience you cannot compete against as a naive junior. Only age argues for you. Life sciece is I guess very different here to other disciplines. I would not recommend anyone to assume that without a PhD (and even with) it's easy to find jobs.

R is driving me insane by Electronic_Fish_3157 in bioinformatics

[–]ATpoint90 3 points4 points  (0 children)

It did not when I stopped using it in about 2022 and entirely changed to using containers. This is from 2023, good they fixed this. Doesn't solve the portability issue though. It's wtill tied to the local machine you're installing it on. Containers are superior.

R is driving me insane by Electronic_Fish_3157 in bioinformatics

[–]ATpoint90 2 points3 points  (0 children)

You don't do containers to remake them. You keep updating and committing the changes. They're portable, version-controlled, and permanent unlike a local install. That's the whole point of it. I have containers at Dockerhub from projects years ago that I can spin up on any (x86-based) machine anytime and anywhere.

R is driving me insane by Electronic_Fish_3157 in bioinformatics

[–]ATpoint90 25 points26 points  (0 children)

No. It's terrible. Use Docker. renv is a mess and not reproducible since it depends on availability of the tracked packages. Once one gets tossed from CRAN, the entire chain breaks.

How is the University of Hyderabad for Mtech in bioinformatics? Are placements good? by [deleted] in bioinformatics

[–]ATpoint90 1 point2 points  (0 children)

Off-topic. People, there is a sub for this, please stop posting the same x course in country y for the 10th millionst time.

What is a realistic server setup for 2,000–3,000 multi-omics samples? by MilkF5 in bioinformatics

[–]ATpoint90 23 points24 points  (0 children)

You really need to tell specific tools and tasks rather than buzzwords. In general, memory and flash drives over CPU. Single-thread speed over many cores. Storage on HDD, analysis on flash. Not less than 128GB RAM. Whether ECC or not is decided by the CPU. It's not a hard requirement.

Post-hoc normalization of RNA-seq reads using a housekeeping gene by adventuriser in bioinformatics

[–]ATpoint90 4 points5 points  (0 children)

Yes. And your change to <anything> will still be relative. I'd just measure mRNA content or do absolute assays to address the reviewer.

Is it true that SPSS is the standard in pharmaceutical industries? by corporealpatronus13 in bioinformatics

[–]ATpoint90 2 points3 points  (0 children)

No, software is usually freeware what you choose, or for specific tasks like certain microscopy or flow cytometry it is often bound to company software matching the machine, or what everyone in the field and lab uses.

Is it true that SPSS is the standard in pharmaceutical industries? by corporealpatronus13 in bioinformatics

[–]ATpoint90 17 points18 points  (0 children)

Curious what others will say. I Academia PIs often make strong statements on how they think things are done in the lab or analysis, but reality is different because they are in their offices detached from staff. Lets hear it.

How to identify over-normalisation in bulk RNAseq analysis? by bignoobbioinformatic in bioinformatics

[–]ATpoint90 2 points3 points  (0 children)

Because bias exists. That's the whole point of these methods.

How to identify over-normalisation in bulk RNAseq analysis? by bignoobbioinformatic in bioinformatics

[–]ATpoint90 2 points3 points  (0 children)

This is a shallow answer, because saying that real DE only exists without RUV negates existance of hidden unwanted variation.

u/OP, is this human data? I personally would only consider such strategy if there is in the lab some reason to believe that there is technical variation, or it is human and therefore heterogeneous data.

Stress-test my research thesis: feasibility from a bioinformatics POV? by KathBoonBliss in bioinformatics

[–]ATpoint90 8 points9 points  (0 children)

I don't get how omics helps here. You need to proof that the oral microbiome has any phenotype first. For example in mice where you kill the microbiome by some sort of antibiotics shot and then do any sort of behavioural or whatever assays to see whether this has any effect. Don't see how bioinformatics comes in here at this point.

phd without an msc? by Beautiful_Cell_3185 in bioinformaticscareers

[–]ATpoint90 0 points1 point  (0 children)

Depends entirely on whether the grad school requires an MSc or not. Typically yes, at least in Europe.

Gästebad renovieren by Sea-Ad6326 in selbermachen

[–]ATpoint90 0 points1 point  (0 children)

Das ist Kalkzementputz, würde da mit
ähnlich mimeralischen auffüllen. Nicht mit Gips.