Questions tagged [matlab]

MATrix LABoratory. A scripting language similar that is popular in modelling and image analysis, as well as bioinformatics and other fields. The language is particularly well suited for common matrix and array operations.

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Using PANDA to infer gene regulatory networks without ppi

I'm using this tutorial ( to use PANDA to infer gene regulatory networks, but without ppi values (which I've been told can be ...
Feynman's user avatar
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2 votes
2 answers

PWM (4xM matrices) to Sequence Logo Visualizations in MATLAB or Python

Is there a MATLAB, or else Python (not R) tool for visualizing sequence Logos from probability weight matrices (PWMs)? This seems like a basic and simple tool to implement, yet just above the ...
Zebra Fish's user avatar
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Cobratoolbox unable to identify gurobi solver when passing initCobraToolbox

I am running into this issue lately when I am trying to install the Cobratoolbox on matlab along with having installed the prerequisite gurobi solver and adding it to the MATLAB path. I have run the ...
Dave's user avatar
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How to assess if this strategy is good to have some phylogenetic information?

I have several organisms and I want to calculate for each one of these their codon composition implementing a pairwise distance matrix between these codon vectors to build a phylogenetic tree. ...
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How to implement SEG (Wootton and Federhen ,1993) algorithm?

I want to implement SEG in my MATLAB environment and I'm relying on Wootton and Federhen (1993) Reading the article I cannot succeed to understand what kind of process I have to implement in order to ...
Spartan 117's user avatar
2 votes
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What does that mean if there is no bifurcations in my time series single cell data?

Sorry, I have analysed my time series single cell data with Scuba algorithm but that says that there is no bifurcations in my data and outputted a single chain of 4 states with no branching like ...
Angel's user avatar
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4 votes
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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 ...
wgrt's user avatar
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3 votes
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Large range parameter identification

I have a model (ODE) of an enzymatic reaction, and I'd like to estimate four of its parameters to fit some available data. To obtain the model I am just using Mass-Action Kinetics. Some more details: ...
PepeToro's user avatar
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3 votes
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Error in creating a volcano plot in MATLAB

I am a complete newbie to MATLAB and the first task I have is to create a volcano plot. I have been using this link to understand about it and get started. I tried to run it on dummy values - ...
user1993's user avatar
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