8 votes
Accepted

What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it PCR?

It may be necessary to distinguish between methods that use unique molecular identifiers (UMIs), such as 10X's Chromium, Drop-seq, etc, and non-UMI methods, such as SMRT-seq. At least for UMI-based ...
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  • 561
7 votes

What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it PCR?

The Biostars thread turned out helpful. The most interesting possible cause, not mentioned in the Ian Subery's answer, is that due to bursty nature of transcription, the true distribution of ...
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5 votes

What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it PCR?

I know of no references for this, but in general, I would say that your reasoning is sound. I would just add that in contrast to what I suspect you have simulated, not all transcripts are equally ...
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  • 3,221
4 votes

How can I translate infix to mathml using the python interface to libsbml?

It’s quite straightforward to convert infix to mathml using libsbml. Make sure you have libsbml installed in python by typing pip install python-libsbml at the ...
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  • 251
4 votes

Expected allele frequency distribution of SNVs in real NGS data

I don't have enough experience to answer which probabilistic distribution should be used. However, this questions also also asks how to estimate parameters of the distributions. If a binomial ...
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  • 2,096
3 votes
Accepted

Hierarchical models with limma?

Yes, you can use limma for this mixed model approach. Like you suggest, the random effect (persons) can be put in duplicateCorrelation(). Here is a similar example with RNAseq data, on bioconductor ...
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  • 3,551
2 votes

Does SBOL require representing intermediate products like mRNA?

As far as I understand, the purpose of SBOL is not to create a comprehensive model, but to communicate a design. So the question you have to ask is "is the mRNA part of my design, or is it an ...
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2 votes

Link Prediction in Bipartite Networks between biological pathways and drugs

I am not sure if I understood correctly how you classify the drugs. But what you attempt to do is similar to what they do here but in that article they use the drugs targeted to a molecule/pathway to ...
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  • 4,622
2 votes
Accepted

How I debug this code?

The problem was I should use ENTREZ rather than gene symbols
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  • 1,697
2 votes
Accepted

How to model the effect of acid/base on pH

I figured that one has to include only the changes in the rules formula. Keeping the initial value of the Species or Parameter ...
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  • 141
2 votes

Is there any tools that can generating FBA model from genome sequences or proteome sequences?

To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have ...
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  • 4,622
2 votes

How do I build a glycosylated protein from PDB files manually?

You can use ChimeraX. Open your glycans and your protein pdb files as different models, then move the models of your glycans until they are near the residues you want (in the Toolbar: Right Mouse -&...
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1 vote

How do I build a glycosylated protein from PDB files manually?

answer from @coot, converted from comments (please edit this answer to improve it if you can): Manual model building is a common thing in structural biology. Usually, Coot is used.
1 vote

How to use multiple .pdb files as templates for homology modelling?

AlphaFold2 You are asking about how to hybridise different threaded models, but I would not give up on AF just yet as it can do complexes. AlphaFold2 is conceptually amazing, but does have some issues ...
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  • 3,719
1 vote

Visualizing cell growth

I would recommend looking into Python's plotting utilities, for example here. I would recommend specifically looking at the examples that plot mathematical functions. The basic idea is that you ...
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1 vote

Tools for modelling and visualizing growth of cells

If the scenario is simpler, and you can't find anything by searching, I would consider just writing your own. The modelling can be done in any language but if compute time is an issue - for example ...
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  • 901
1 vote

How I deal with this expression set?

Look up a tutorial on DESeq2. To keep things simple for your first time, I'd reduce your phenotypes to "high" and "low" bins instead of trying to use the cell count numbers as they are. Then once ...
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  • 1,672
1 vote

How to verify if the stationary states of a biological model are correct?

After much analysis of the model, I came to the conclusion that I will not be able to verify how the equilibrium points behave graphically. Since you will have to create a phase diagram in R ^ 5, ...
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  • 51
1 vote

Mathematical notation for formulating a rank score

Here is my solution to the problem. I am posting it here in case anyone else come up with the same idea but did not know how to formulate it in mathematical notation! $$ \psi_i = \sum_{i=1}^9 S_i $$...
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  • 181
1 vote

How are PDO and PDX used in computational and predicative models for tumour biology?

Potential pitfall! I'm not sure about predictive models, but you need to be aware of a potential pitfall in blindly aligning PDX or PDO based sequencing data without first removing contaminating host ...
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  • 1,029

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