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9 votes
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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 ...
merv's user avatar
  • 651
8 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 ...
Martin Modrák's user avatar
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 ...
Ian Sudbery's user avatar
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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 ...
winni2k's user avatar
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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 ...
rhody's user avatar
  • 251
3 votes

Why can't AlphaFold predict the consequences of point-mutations?

Other have addressed why AlphaFold2 cannot really get the necessary signal from MSA (Multiple Sequence Alignment) and memory to properly model a variant, but I thought I'd add my observations/rants. I ...
Matteo Ferla's user avatar
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3 votes
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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 ...
benn's user avatar
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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 ...
llrs's user avatar
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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 -&...
O.Laprevote's user avatar
2 votes
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How I debug this code?

The problem was I should use ENTREZ rather than gene symbols
Zizogolu's user avatar
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2 votes
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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 ...
barerd's user avatar
  • 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 ...
llrs's user avatar
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2 votes
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How to prove correlation between gene expression and functions using omics data in bioinformatics?

In general terms data mining is needed, then supervised learning and finally ODE, because you are performing DE against enzyme kinetics and thats doable, but you'll need a lot of biochemical knowledge....
M__'s user avatar
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2 votes
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how to add a custom elements into PyMOL visualization?

my attempt : ...
pippo1980's user avatar
  • 1,088
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 ...
James M's user avatar
  • 135
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

As marcin points out in the comments: by "AphaFold (AF) has not been trained to predict structural consequences of point mutations" it is meant "AF is not able to tell you whether your ...
O.Laprevote's user avatar
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

This answer is from common knowledge rather than specific infield expertise. The question could be more expertly answered by other members. If you really want to pursue this type of calculation, it's ...
M__'s user avatar
  • 12.5k
1 vote

Would duplicate climatic variables impact maxent?

Ok I understand better now so I'll write an answer. Look at the bioclimatic data site. You can download them from the main page, but the suggestion to generate them from the time series data using an ...
Maximilian Press's user avatar
1 vote

Advise on building an effect ML model for predicting important proteins for drug response

The missing values might be an issue indeed. You might want to use imputation methods, e.g. ...
rkellerm's user avatar
  • 113
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 ...
Matteo Ferla's user avatar
  • 4,234
1 vote

Determining significance of a variable in a glm model

Second viewing of the question from what I can see -0.22 as a coefficient of origin is a strong negative association, so yeah it has a major impact. Its not how I would have done it, but that looks to ...
M__'s user avatar
  • 12.5k
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 ...
Maximilian Press's user avatar
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 ...
jgreener's user avatar
  • 941
1 vote

Comparing phylogenetic models with different datasets

The key issue is the data is subject to reticulation, languages are seldom clean breaks. In nucleotide data this can be identified due to deviations from physical linkage and call it recombination. ...
M__'s user avatar
  • 12.5k
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 ...
swbarnes2's user avatar
  • 1,921
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, ...
wgrt's user avatar
  • 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! $$ \psi_i = \sum_{i=1}^9 S_i $$...
RJF's user avatar
  • 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 ...
Matt Bashton's user avatar
  • 1,069

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