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Update 03-horizontalGeneTransfer-TDA.md
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nselem authored Jul 29, 2024
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Expand Up @@ -354,7 +354,7 @@ We want to investigate whether the resistance genes present in the
first pangenome of _S. agalactiae_ are the product of vertical inheritance, or
other processes could be involved.

> ## Exercise 1(Begginer): Manipulating dataframes
> ## Exercise 1(Beginner): Manipulating dataframes
> Dataframes
> Ask [ChatPGT](https://chat.openai.com/) or consult [stack over flow](https://stackoverflow.com/) about the following dataframe functions
> 1) how to load data in dataframe from a link
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~~~
{: .output}

> ## Exercise 2(Begginer): Persistent homology of _S. agalactiae_ resistome
> ## Exercise 2(Beginner): Persistent homology of _S. agalactiae_ resistome
> Fill in the blanks with the following parameters to calculate the persistent homology of the _S. agalactiae_ resistome.
> hamming_matrix_3, values, calculate_hamming_matrix, create_complex
>
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> {: .solution}
{: .challenge}

> ## Exercise 3(Begginer): Plot the persistent barcode of _S. agalactiae_ resistome
> ## Exercise 3(Beginner): Plot the persistent barcode of _S. agalactiae_ resistome
> Chose the right parameters to plot the persistence diagram of _S. agalactiae_ resistome.
> <a href="../fig/tda_04_barcode_strep.png">
> <img src="../fig/tda_04_barcode_strep.png" alt="Bacode population with hgt" />
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