Questions tagged [modelling]

Assignment of data into a defined mathematical description invariably associated with a priori assumptions

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Comparing phylogenetic models with different datasets

I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...
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Flux balance Analysis, Result interpretation, solver Solver Heuristics

i am new to modelling of cellular networks, and I have two basic questions, regarding the result interpration. I am using the COBRAToolbox to do a flux balance analysis of a whole genome scale model ...
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What is coarse-grained modeling of proteins?

I need beginner-level study materials for coarse-grained modeling of proteins. Can anyone supply me with entry level resources besides the Wikipedia article? Background Coarse grain protein modelling ...
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Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?

I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
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Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
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1 vote
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146 views

length of 'dimnames' [1686] must match that of 'dims' [3]

Please if anyone has experience with the use of the BSEQ-SC package for the deconvolution of bulk RNA sequencing data with single cell RNA sequencing data I will be very grateful for your suggestion. ...
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Interlink among different length scales of simulation and modelling techniques

I found this figure in the following paper A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites However, I am skeptical about its correctness, as this paper is not peer-...
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GSM Modelling Issues. Problems replicating results during FBA/FVA Optimization

recently I've decided to start learning about GSM and I am currently applying them to a practical scenario of cyanobacteria metabolic engineering. I am trying to perform FBA and FVA analysis of a ...
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Selecting genes with more contribution from PCA

I have RNA-seq data in response to treatment vs non response; By machine learning I selected three principle components likely can predict the response based on the gene expression. Now I have ...
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