15  LaTeX Document Preparation

LaTeX is the standard for academic writing, especially in fields with mathematical notation. Claude Code can make LaTeX significantly more approachable.

15.1 Why LaTeX?

  • Professional typography: Beautiful equations, consistent formatting
  • Reference management: BibTeX handles citations automatically
  • Version control friendly: Plain text works well with git
  • Journal requirements: Many journals provide LaTeX templates

15.2 Getting Started with LaTeX

If you don’t have LaTeX installed:

> Help me install LaTeX on my system

Mac:

brew install --cask mactex

Windows: Download MiKTeX from miktex.org

Linux:

sudo apt-get install texlive-full

15.3 Setting Up a LaTeX Project

> Create a LaTeX project for a scientific paper with:
> - Main document
> - Separate file for references (BibTeX)
> - Folder for figures

Claude creates:

paper/
├── main.tex
├── references.bib
├── figures/
└── sections/
    ├── introduction.tex
    ├── methods.tex
    ├── results.tex
    └── discussion.tex

Sample main.tex:

\documentclass[11pt]{article}

\usepackage{graphicx}
\usepackage{amsmath}
\usepackage{natbib}
\usepackage{hyperref}

\title{Your Paper Title}
\author{Your Name}
\date{\today}

\begin{document}

\maketitle

\begin{abstract}
Your abstract here.
\end{abstract}

\input{sections/introduction}
\input{sections/methods}
\input{sections/results}
\input{sections/discussion}

\bibliographystyle{plainnat}
\bibliography{references}

\end{document}

15.4 Common LaTeX Tasks

15.4.1 Writing Equations

> Help me write the equation for logistic regression in LaTeX
\begin{equation}
P(Y=1|X) = \frac{1}{1 + e^{-(\beta_0 + \beta_1 X_1 + ... + \beta_n X_n)}}
\end{equation}
> I need a system of equations for a differential equation model
\begin{align}
\frac{dS}{dt} &= -\beta SI \\
\frac{dI}{dt} &= \beta SI - \gamma I \\
\frac{dR}{dt} &= \gamma I
\end{align}

15.4.2 Creating Tables

> Create a LaTeX table from this data:
> Gene | Control | Treatment | p-value
> BRCA1 | 2.3 | 5.7 | 0.001
> TP53 | 4.1 | 3.9 | 0.45
\begin{table}[h]
\centering
\caption{Differential expression results}
\begin{tabular}{lccc}
\hline
Gene & Control & Treatment & p-value \\
\hline
BRCA1 & 2.3 & 5.7 & 0.001** \\
TP53 & 4.1 & 3.9 & 0.45 \\
\hline
\end{tabular}
\label{tab:de_results}
\end{table}

15.4.3 Including Figures

> Add a figure from figures/umap.pdf with a caption about cell clustering
\begin{figure}[h]
\centering
\includegraphics[width=0.8\textwidth]{figures/umap.pdf}
\caption{UMAP visualization of single-cell data revealing distinct cell populations.
         Cells are colored by cluster identity.}
\label{fig:umap}
\end{figure}

15.4.4 Managing References

> Add this paper to my BibTeX file: DOI 10.1016/j.cell.2015.05.002

Claude fetches the citation information and creates:

@article{macosko2015highly,
  title={Highly parallel genome-wide expression profiling of individual
         cells using nanoliter droplets},
  author={Macosko, Evan Z and Basu, Anindita and Satija, Rahul and ...},
  journal={Cell},
  volume={161},
  number={5},
  pages={1202--1214},
  year={2015},
  publisher={Elsevier},
  doi={10.1016/j.cell.2015.05.002}
}

15.5 Troubleshooting LaTeX Errors

LaTeX error messages can be cryptic. Claude Code helps:

> I'm getting this error when compiling:
> ! Undefined control sequence.
> l.45 \includegraphics

Claude identifies: “You need to add \usepackage{graphicx} to your preamble.”

> My references aren't showing up, just [?] marks

Claude guides you through the BibTeX compilation process:

pdflatex main
bibtex main
pdflatex main
pdflatex main

15.6 Journal Templates

> I need to format my paper for submission to Nature Methods.
> Help me set up their LaTeX template.

Claude helps you: 1. Find and download the official template 2. Restructure your content to fit 3. Adjust formatting requirements

15.7 Converting to/from LaTeX

15.7.1 Word to LaTeX

> Convert this Word document to LaTeX, preserving citations and figures

15.7.2 LaTeX to Word

> Convert my LaTeX paper to Word format for a collaborator

Using pandoc:

pandoc main.tex -o main.docx --bibliography=references.bib

15.8 Automating Compilation

> Create a Makefile for compiling my LaTeX document
MAIN = main
BIB = references

all: $(MAIN).pdf

$(MAIN).pdf: $(MAIN).tex $(BIB).bib
    pdflatex $(MAIN)
    bibtex $(MAIN)
    pdflatex $(MAIN)
    pdflatex $(MAIN)

clean:
    rm -f *.aux *.log *.bbl *.blg *.out

.PHONY: all clean

15.9 Tips for LaTeX with Claude Code

15.9.1 Let Claude Handle the Syntax

> I want a matrix with 3 rows and 3 columns showing the values...

Don’t memorize LaTeX syntax—describe what you want.

15.9.2 Debug Incrementally

If compilation fails after many changes:

> Compile after each change to identify which one broke it

15.9.3 Use Version Control

LaTeX is plain text—perfect for git:

> Commit the current working version before making major changes

15.10 Next Steps

Continue to Automating Repetitive Tasks.