Underlines

\underline{Text}

A better approach https://alexwlchan.net/2017/10/latex-underlines/

Footnotes

Within text, add a reference to the footnote item

RiboPlot \ref{itm:riboplot}

Then, add item to the footnote list at the end of the document

\begin{enumerate}
\item \label{itm:riboplot} 
\href{https://github.com/vimalkvn/riboplot}{RiboPlot}
\end{enumerate}

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