8

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 methods, the alternative perspective, that there is no significant zero-inflation in scRNA-seq, is also advocated in the single-cell research community. The ...


6

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 transcript counts across cells can be bimodal with a peak at zero even assuming a simple model of transcription such as the random telegraph model. See for example ...


5

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 likely to be captured and amplified. We don't really understand what the determinants of this are, but for example, GC content is definitely related.


4

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 windows/Mac/Linux command line or !pip install python-libsbml if you are running a Jupyter notebook. Some tools such as Tellurium already have libsbml preinstalled. At the python command line ...


4

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 distribution is chosen, then Heng Li's paper titled "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical ...


3

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 support site.


2

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 implicit part of the biology which does not help to convey what I'm trying to build?". I think your summary is a giveaway: For example, let's say that I'm ...


2

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 find combination of drugs that are better for the disease (not an alternative drug), see the first image: In that article they mention the pathway cross-talk ...


2

The problem was I should use ENTREZ rather than gene symbols


2

I figured that one has to include only the changes in the rules formula. Keeping the initial value of the Species or Parameter when defining circular or self-referencing formulas caused the error. So the correct rule becomes: pH=-a*Acid instead of pH=pH-a*Acid or pH=7.4-a*Acid. For convenience, I include the correct code crowded with several reactions ...


2

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 enough knowledge, time and computationally power to do this. At the moment I'm only aware of a paper simulating the Mycoplasma genitalium cell. But I'm not sure it ...


1

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 to such an extent that I blogged about common problems I was getting so many questions. Specifically, it models one protein chain in isolation. In the ...


1

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 create a function that computes your equation based on the different parameters as inputs ($a, a_{max}, l_{max}$) and then you can plug in a range of values for ...


1

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 you want to run a simulation with many cells or many simulations - then I would use a language that can support that such as Julia or NumPy in Python. In fact ...


1

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 you understand what the software is doing, you can get fancier.


1

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, there are five equations, and I can not do two-to-two comparison in these cases, because I will always have a function that depends on a variable that will not be ...


1

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! $$ \psi_i = \sum_{i=1}^9 S_i $$ where $S_i$ is the score function and defined as: $$ S_i = \cases{ 0 & \text{if $\theta(x_i) < Q_1$ or $\theta(x_i) = $ benign/neutral} \\ ...


1

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 organism reads, as otherwise these will lead to a lot of false positive variants caused by miss alignment. In my experience even a small mount of host ...


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