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 (https://github.com/netZoo/netZooM/blob/master/tutorials/panda/panda.pdf) to use PANDA to infer gene regulatory networks, but without ppi values (which I've been told can be ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
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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 -
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