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Questions tagged [modelling]

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1
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2answers
69 views

How I debug this code?

I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error ...
2
votes
1answer
47 views

How to model the effect of acid/base on pH

I would like to model a biological compartment with sysBio R package. It is fine but I'm having a difficult time with modeling the change in pH due to acidosis. I tried several things like: ...
0
votes
0answers
54 views

Making a model of gene contribution in cancer diagnosis

I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders; I have done differential expression by DESeq2 and I obtained a ...
3
votes
1answer
36 views

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

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them? What I was thinking is more like to ...
3
votes
1answer
108 views

Hierarchical models with limma?

I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
5
votes
1answer
73 views

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

I'm mathematically modeling yellow fever, and yet, after assembling the model, I need to find the stationary states of the model. I had to do it by hand because wolfram software could not get the ...
2
votes
1answer
64 views

Link Prediction in Bipartite Networks between biological pathways and drugs

Currently I'm building a big matrix (using microarray, mass spectrometry, RNAseq data) that consist by pathways (rows) and treatment/drugs (columns). The values of that matrix are scores that ...
16
votes
3answers
354 views

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

First, sorry if I am missing something basic - I am a programmer recently turned bioinformatician so I still don't know a lot of stuff. This is a cross post with a Biostars question hope that's not ...
4
votes
0answers
82 views

Differences between TM and GDT-TS scores for structure comparison

What are the relative advantages / disadvantages of the TM (template modelling) and GDT (global distance test, total score) scores, used in protein structure prediction competitions, such as CASP? ...
0
votes
1answer
103 views

Mathematical notation for formulating a rank score

This is a cross-post from Mathematics forum. As no one has answered it yet, I fIgured post here as well. I would like to describe a transform I used to rank my data points. I have recoded my variable ...
3
votes
1answer
137 views

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

There are 2 new wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases/resources/computational ...
9
votes
1answer
114 views

Expected allele frequency distribution of SNVs in real NGS data

I have a huge amount of ~20x human WGS samples, aligned, and all SNVs that were called with GATK under standard germline parameters set. What I need to do is to model SNVs Allele Frequency (AF) for ...