This is a five-part tutorial to help academic researchers get started on Claude Code.
I have written it an accessible language and you don't need any technical background to understand this tutorial or use Claude Code.
Part 1: What Is Claude Code?
Claude Code is a tool that runs on your computer. Don’t be intimidated by the word “code.” You don’t need any coding or programming skills to use it. You install Claude Code on your computer just like you would an app like Zoom or Zotero.
Once you have it on your computer, you open your project folder (dissertation, paper, etc.) and let Claude work inside the folder. Claude can read every file in the folder, edit existing files, and create new ones. It can also remember what you were working on after you end a session.
Unlike browser-based apps like ChatGPT and Gemini that only “talk,” Claude Code can actually “do” things for you.
1.1 Why You Should Care About It?
You are a researcher and have a folder on your computer with several PDFs, drafts of your papers, spreadsheets, datasets, and a few transcripts of interviews. All these documents are relevant to your project, but you need to make connections across published literature, gathered data, and your own notes.
This is the kind of use-case that Claud Code was built for.
Most academics and researchers have used AI apps in their browsers (ChatGPT, Claude, Gemini, etc.) You open a tab and type in a prompt and the AI replies. If you want to ask questions about your papers or drafts, you add them to ChatGPT or Claude.
Claude Code is different because instead of you bringing your files to an AI app in the browser, you bring the AI into the folder containing all your data.
1.2 Why Claude Code Matters for Academic Work
There are two fundamental ways in which Claude Code can work as your reliable and powerful research assistant.
First, Claude Code remembers you, your research, your writing style, and your ever-evolving research requirements. You won’t have to explain your requirements repeatedly.
Second, since Claude Code works within a folder on your computer, it can process multiple files at a time. For example, it can go through all forty-five PDFs in your folder and extract relevant information (objectives, methodology, etc.) from all of them. You can even ask it to create a new file based on extracted information.
Claude Code can handle all types of files from Word files to Excel sheets, PDFs, etc.
1.3 What Does It Mean in Practical Terms?
If you are a qualitative researcher, load a folder full of interview transcripts and ask Claude Code to give you every instance of a particular utterance, e.g. how each participant talked about a given subject. Then ask it to look for overarching themes across interviews.
If you are a quantitative researcher, add a messy CSV or an Excel sheet in your folder and ask Claude Code to clean it up for you. You can ask it to run descriptive statistics or ask it to explain a critical comment made by a reviewer.
1.4 What Claude Code is Not
Claude Code is an incredibly powerful tool, but it is not a replacement for your expert judgment. It can draft, summarize, code, but what counts as argument or evidence is your responsibility.
Academics who are likely to succeed using Claude Code are the ones who treat it as a research assistant and not those who outsource all their thinking and judgment to it.
Part 2: Installing Claude Code App, Your First Session
If you’re new to Claude Code, set aside 15-20 minutes to install it and set it up. You don’t need any coding skills to use Claude Code.
You will need a Claude Pro or Max subscription to use Claude Code on your computer.
2.1 Installation
Claude Code is available for both Windows and Mac. Go to claude.com/download and download the version compatible with your computer. Run it the way you would any other installer (e.g. Zoom, Zotero, etc.). On Windows, it appears in your Start Menu. On Mac, it appears in your Applications folder.
Open the app once you have installed in it. The first time you open it, Claude will ask you to sign in through browser. Once you have signed in, you will see a column on the left and a chat panel in the middle. The left column will show you a record of all your conversations just like in Claude or ChatGPT in browser.
2.2 Opening Your First Folder
Click “Open Folder.” It usually on top of the chat bar in the main panel. Its position keeps changing slightly with every update, but you will mostly find it in the vicinity of the chat bar.
Navigate to any folder on your computer in which you have stored PDFs or your drafts. If you want to be extra careful, create a dedicated “Claude Research Assistant folder” and navigate to that.
Now Claude Code is inside that folder. It has access to every file and subfolder inside the main folder.
2.3 What a Session Looks Like
A session is the conversation you have with Claude in the main chat panel just like you do it in browser apps like ChatGPT.
The interaction is like browser-based apps like ChatGPT. The only difference is that now Claude Code has access to your files on your computer. It also has the ability to create files on your computer.
Once you are in the folder, give Claude a simple prompt like:
Read all the papers in the folder and give me their main arguments as a separate file.
That’s it. Most of your interaction with Claude Code would be writing instructions like this.
Claude Code will go ahead and retrieve relevant information from the papers and start creating a new file. This file will show up in the folder that you are working in.
As it proceeds, it will ask you for permission to do so. You can make Claude Code bypass permissions, but in the beginning, it’s a good idea to make Claude Code ask for permissions. You don’t want Claude Code to end up deleting any important files without asking you.
Every session you start in Claude Code is automatically saved in the panel on the left.
Part 3: Claude Code as Your Research Assistant
Every time Claude Code starts, it immediately looks for a file called CLAUDE.md for a set on of instructions to follow. Notice the block letters, this is important.
There are two ways you can create a CLAUDE md file: automatic and manual.
3.1 Manually
If you want to do it manually, open Notepad on Windows or TextEdit on a Mac and write down the kind of instructions you want Claude Code to follow. Please note that you only need to write these instructions in plain language. You don’t need to use any coding or programming language.
You can divide CLAUDE md file into following sections:
#Role (the hash sign here indicates that it’s a heading)
Describe the kind of role you would like Claude Code to assume as your research assistant. Give it a few details about your research field and current project.
Describe academic standards relevant to your field of research. For example, you can tell Claude Code to follow a given citation style or a specific structure of a research paper.
#Writing Style
Tell Claude Code the kind of writing style you would like it to follow, whether you want it to respond in academic style or in an informal style.
#Critique Style
Describe how you would like Claude Code to critique your work, whether you would like to focus on your argument, evidence, or methodology.
Save the file as CLAUDE.md in your main Claude folder on your computer and you are done.
You don’t need to have a perfectly crafted CLAUDE.md file. You can always go back and edit it as your project evolves.
3.2 Automatically
If you don’t want to create a CLAUDE.md file manually, simply start a chat session in Claude Code and give it details about its role, standard, writing style, and critique style. Then ask it to create a CLAUDE.md file using this information.
Claude Code will create the file and save it to your Claude folder.
3.3 Auto-Memory
As you work through your project, Claude Code will write short notes about your work and save them for its own use. You won’t see them and you don’t need to bother about them too much. Claude Code puts these notes in a folder and manages it on its own.
Each time you start a session, Claude Code reads CLAUDE.md and its own notes and uses them to answer your questions.
Over time, your instructions and Claude Code’s notes gives it enough context about you and your work that it becomes a reliable research assistant.
You can ask Claude Code about its memory by typing “Tell me what you have stored in your memory.” If a certain piece of information is outdated (e.g. a citation style), simply ask it update its memory with the new information.
3.4 What Not to Put in CLAUDE.md
Don’t put any confidential information in CLAUDE.md or anything that you don’t the AI to use.
Don’t let CLAUDE.md become a set of outdated information because that will have considerable impact on its output. You may want to update the file every few weeks.
Part 4: Working with Your Research Documents
A Claude folder does not have to be very neatly organized. This doesn’t mean you start putting irrelevant files in this folder. What it means is that you should not spend any time organizing it. Claude can do that itself. The only thing you may want to keep in mind is not to give your files confusing names like Dissertation (final) (final2) (use this one).
Add a bunch of PDFs, Word files, datasets, interview transcripts, etc. related to your project.
Suppose you have twenty research papers related to your research topic and you want to find a common theme that runs across all of them. Or maybe you have a certain claim or an argument, and you are looking for papers that present evidence supporting or contrasting that claim.
Open the folder in Claude Code and write a prompt like:
Read every PDF in this folder and tell me which articles disagree with the following argument: [paste the argument here]
Claude will read all the PDFs in the folder and will give you the relevant information from these articles. Claude’s answer may be in the form of a table.
4.1 Research Assistant for Literature Review
If you are a biomedical researcher or a social scientist who frequently runs systematic reviews, download fifty research articles and put them in a folder titled “Systematic Review with Claude.”
Open the folder in Claude Code and give it your screening (inclusion/exclusion) criteria and ask it to screen all the papers in the folder.
Claude Code will screen the papers according to your criteria and give you the results in the form of a table.
4.2 Working with Transcripts
If you are qualitative researcher, you can add interview transcripts in the Claude folder and ask it extract information related to a given topic.
For example, you can ask it to extract how each respondent answer a given question.
4.3 Give Claude a Tedious Task
Put fifty-odd PDFs in a folder and open it in Claude Code. Then ask it to go through them all and rename them using their titles.
You will see that Claude Code has done the needful in a couple of minutes.
4.4 Asking Claude Code to Create Files
Since your project is going to evolve, you would want Claude Code to create certain files for you too so that can you go back to them if needed. It will also help Claude Code with easy retrieval as the project develops.
Anytime you ask Claude Code to do a significant task like screening papers or extracting information from transcripts, ask it to save your answer in folder as a file.
Generally, Claude Code will save these files as markdown (md), which take up very less space and are very easy for Claude Code to retrieve information from. But you can also ask it to create a Word file or an Excel sheet.
Part 5: Claude Code “Skills”
A Skill is a set of instructions that makes Claude Code a specialist for one task. Just like CLAUDE.md file, a Skill is also a markdown file written in plain English. And just like CLAUDE.md, you can create a Skill file both manually and automatically.
Once you create a Skill, Claude Code will remember when to use it. You do not have to remember yourself. But you can always invoke a Skill if want to, by using the forward-slash command.
The easiest way to create a Skill is to ask Claude Code to do it for you. Let’s say, you have regular Zoom calls, and you have transcripts of those calls. For every call or transcript, you want to extract actionable items or things to do.
To create a Skill, start a Claude Code session and simply ask it to create a Skill for extracting actionable items from Zoom transcripts.
Claude Code will get to work. It will ask you follow-up questions and create a Skill file that you can edit if you want to. Maybe you want Claude Code to follow a specific structure while responding.
Once the Skill is created, restart Claude Code and the Skill will be ready to use.
5.1 Difference between CLAUDE.md and Skills
CLAUDE.md contains global instructions about you and your project. It gives Claude Code the big picture about you and your research.
Skills, on the other hand, are meant for particular tasks. These files contain information that are much more specific and granular. CLAUDE.md, Skill, and auto-memory work in concert to give you the best possible response.
What Not to Delegate to Claude Code
Claude Code is great at labor intensive, time consuming, and repetitive tasks. Outsource these tasks to Claude Code. But Claud Code will not be able to create what actually counts as scholarship because it won’t be able to give you new and original arguments.
It can synthesize information that you can then use in service of your argument, but the job of coming up with an original argument remains yours as a researcher.
