Forum: Any good idea for bioinfo final presentation?
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gravatar for anran04100
9 weeks ago by
anran041000
anran041000 wrote:

last semester, we've learn how to analyse date by R on our bioinformatics class. Our class basically focused on the idea of analysing the data of multi-mics, my classmates have already choosed the topic of PCA, PLS, tSNE and WGCNA. Does anyone could suggest me a good topic according to this? I do really have trouble in choosing things, this presentation is so essential for me. Please guys, I am kind of exhausted. THX!

forum R • 221 views
ADD COMMENTlink modified 9 weeks ago by Carambakaracho2.2k • written 9 weeks ago by anran041000

How to contribute to Bioconductor

ADD REPLYlink written 9 weeks ago by russhh5.5k

seems most of them are dimension reducing tools / classifiers to me. You can pick up classifiers such Random forest, CART, SVMs, Lasso regression etc.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by cpad011213k
1
gravatar for russhh
9 weeks ago by
russhh5.5k
UK, U. Glasgow
russhh5.5k wrote:

This thread may get closed because you have shown relatively little effort.

But before it does, I think it's important that you identify part of bioinformatics, or part of the R/bioconductor ecosystem that is important/interesting to you. It will be extremely hard for you to write an interesting talk on something unless that something sparks an interest for you.

Could you expand upon the purpose of the talk and give an outline of what the expected contents of the talks should be:

  • are you to present a data-analysis of your own,

  • are you to summarise a data-analysis method,

  • are you to able to discuss the software design / architecture underpinning this stuff,

  • are you able to discuss the social aspects or the publication aspects of coding and releasing packages.

You should take a step back and think about what the challenges in bioinformatics are in 2020, and (based on your question) how does R solve those problems. For me the biggest challenge is reproducibility.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by russhh5.5k

First of all, I do appreciate your suggestions.

Since this is my first year of college, I didn't start my own data-analysis. So, I'm going to introduce a type of method to anaylse data. I think I am gonna focus on multi-omics, but there are so many things I don't know that well so it kind of got me there. Maybe I can introduce a package in Bioconductor.

Thanks for your generous ideas.

ADD REPLYlink written 9 weeks ago by anran041000

I admit, had you asked me the questions above at the level of the OP with the breadth of bioinformatics today, I was overwhelmed, too and I started when Koonin's COGs where bleeding edge...

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Carambakaracho2.2k
0
gravatar for Carambakaracho
9 weeks ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:

I'm not the best source, as I'm behind on most of the active research, but I remember the feeling. For beginners it's not so easy to separate the wheat from the chaff, imo this would be your teacher's responsibility, though.

Let me give it shot: for data analysis milestones comparable with what you mention are

None of this is trivial, though, but neither is PCA/PLS/tSNE. Good luck.

ADD COMMENTlink written 9 weeks ago by Carambakaracho2.2k

Carambakaracho : I think OP wants the topic to be related to R since the class is about R.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax87k

bloody **, I should pay attention to details...

Well, technically at least, DESeq2. EdgeR, and limma/voom are R . For what it's worth anyway

ADD REPLYlink written 9 weeks ago by Carambakaracho2.2k
1

Since it's also about multi-omics, maybe something along the lines of uisng limma for RNA-seq vs. limma for metabolomics data.

That being said, maybe presenting on the Bioconductor philosophy of specialized objects for certain data types might be a good exercise (going from Biostrings to RangedObjects to SummarizedExperiment to SingleCellExperiment and MultiAssayExperiment). The power and usefulness of those objects is often only understood once you have to deal with a package outside the BioC universe (yes, Seurat, looking at you [but not just you]!)

EDIT: just wanted to provide a couple of pointers about the different object types:

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Friederike5.9k
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