9
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 ...
- 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 ...
- 403
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 ...
- 3,341
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 ...
- 2,286
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 ...
- 4,254
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 ...
- 3,591
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 ...
- 4,723
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 -&...
- 483
2
votes
Accepted
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 ...
- 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 ...
- 4,723
2
votes
Accepted
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__♦
- 12.8k
2
votes
Accepted
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 ...
- 135
1
vote
Accepted
Deseq2 model formula and longitudinal experimatal (or time-series) designs
There are a few ways to approach your question, as you're partly asking for an opinion on the best method. In my view, to analyze changes in gene expression over time between treatment and control ...
- 148
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 ...
- 483
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__♦
- 12.8k
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 ...
- 4,212
1
vote
Single or partitioned model for supermatrix tree inference?
Okay, you can't concatenate genes into a singular matrix particularly if these are rRNA genes versus protein genes, except in rare situations where the tests say 'thats okay' (below). This is simply ...
M__♦
- 12.8k
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.
...
- 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 ...
- 4,254
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__♦
- 12.8k
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 ...
- 4,212
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 ...
- 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__♦
- 12.8k
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 ...
- 1,971
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, ...
- 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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Only top scored, non community-wiki answers of a minimum length are eligible