> For the complete documentation index, see [llms.txt](https://docs.hits.ai/omicshorizon-user-guide-en/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.hits.ai/omicshorizon-user-guide-en/project/ai-data-analysis.md).

# AI Data Analysis

Analyze multi-omics data by conversing with AI — no coding required.

**All you need to do is describe your research intent in plain language.** The AI Agent selects the appropriate statistical methods, executes the analysis, and automatically generates publication-ready figures and reports.

***

## 1. Uploading Data Files

Upload the data you want to analyze. You can add files directly from your computer or bring in files saved in the library.

### 1.1. Uploading Local Files

{% stepper %}
{% step %}
**Click the \[Add analysis file] button at the bottom right of the analysis screen.**
{% endstep %}

{% step %}
**Select \[File upload].**
{% endstep %}

{% step %}
**When the upload modal opens, select or drag your files to upload.**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2Fb5Y40GNxzVSnBUQqxJDB%2Fimage.png?alt=media&amp;token=7b298ebe-4793-439f-bc56-0c5352aa1efd" alt=""><figcaption><p>File upload modal</p></figcaption></figure>
{% endstep %}

{% step %}
**Click \[Upload files] to attach the file to the current analysis.**
{% endstep %}
{% endstepper %}

{% hint style="warning" %}
Files cannot be added if the combined size of all uploaded files exceeds **10GB**.\
Check file sizes before uploading.
{% endhint %}

### 1.2. Importing from Library

You can bring in files from previous analyses or files shared by your team.

{% stepper %}
{% step %}
**Click \[Add analysis file].**
{% endstep %}

{% step %}
**Select \[Import from library].**
{% endstep %}

{% step %}
**Search or browse the file list and select the files you need.**
{% endstep %}

{% step %}
**Click \[Add.**
{% endstep %}
{% endstepper %}

{% hint style="info" %}
Uploaded files can be viewed in the **\[Added files]** section of the Analysis asset panel on the right. You can download individual files or save them to the library.
{% endhint %}

{% hint style="warning" %}
**Data protection policy**

Uploaded files cannot be deleted. This policy ensures research reproducibility.
{% endhint %}

***

## 2. Setting Up a Workflow

A workflow is a step-by-step analysis plan.\
You can reproduce a published paper's exact methods or save and reuse your own frequently used analysis procedures.

Workflows are optional — you can run an analysis without one.

### 2.1. Extracting a Workflow from a Paper

{% stepper %}
{% step %}
**In the workflow section, select \[Extract from paper].**
{% endstep %}

{% step %}
**Upload the reference paper as a PDF file.**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FrKMj4DDLDmq88HXwsWgm%2Fimage.png?alt=media&amp;token=17fcccea-f2b5-4eed-b4f1-2739f714cc23" alt=""><figcaption><p>Extract from paper — Step 1</p></figcaption></figure>
{% endstep %}

{% step %}
**Click \[Extract workflow].**

The AI reads the Methods section of the paper and automatically extracts the workflow.

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2Fox8KB9J5U9KlwN67RCh4%2Fimage.png?alt=media&amp;token=bfab5d24-cef0-4d26-9b9e-d1fae11f4e39" alt=""><figcaption><p>Workflow extraction in progress — Step 2</p></figcaption></figure>
{% endstep %}
{% endstepper %}

{% hint style="info" %}

* Extracted workflows are automatically saved to the library and can be reused in other analyses.
* PDF files up to **500MB** can be uploaded.
  {% endhint %}

### 2.2. Importing a Workflow from Library

{% stepper %}
{% step %}
**In the workflow section, select \[Import from library].**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FZyP0erkejljWOCdsJnwv%2Fimage.png?alt=media&amp;token=635a23b1-d5b1-4081-8ceb-aadc45a47b5c" alt=""><figcaption><p>Importing a Workflow from Library</p></figcaption></figure>
{% endstep %}

{% step %}
**Select the workflow you want from the saved list.**
{% endstep %}

{% step %}
**Click \[Add] to add it to the current analysis immediately.**
{% endstep %}
{% endstepper %}

### 2.3. Editing a Workflow

An applied workflow can be edited at any time from the analysis chat screen.

{% stepper %}
{% step %}
**Click the \[Edit] button in the workflow display area.**
{% endstep %}

{% step %}
**Edit the content in the workflow edit modal.**
{% endstep %}

{% step %}
**Click \[Apply].**
{% endstep %}
{% endstepper %}

***

## 3. Conversing with AI to Analyze Data

### 3.1. Entering Prompts and Running Analysis

**No commands or code needed — just describe your research intent as you would to a colleague.**

{% stepper %}
{% step %}
**Type your research intent in natural language in the chat input field.**

{% hint style="info" %}
Example inputs:

* "Compare gene expression differences between treatment responders and non-responders in RNA-seq data"
* "Generate a Manhattan plot from this GWAS data and explain the key loci"
* "Analyze my data using the same method as the uploaded paper"
  {% endhint %}
  {% endstep %}

{% step %}
**The AI Agent automatically performs the analysis.**

While the analysis runs, you can see **the current step and what the AI is doing** in real time.

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FgVg6djQDgTJWKlIMvp4Q%2Fimage.png?alt=media&amp;token=bcb56ab3-cd44-4528-98ec-46db993ec918" alt=""><figcaption><p>Analysis in progress — step-by-step status</p></figcaption></figure>

{% hint style="warning" %}
New messages cannot be sent while an analysis is in progress.
{% endhint %}
{% endstep %}

{% step %}
**Review the results and continue with follow-up analyses.**

Along with the results, the AI provides **insights and recommended next steps**.

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FrzMm5ijtW1OAX2bukecM%2Fimage.png?alt=media&amp;token=8013534d-2773-4374-9c2e-795e2f23f2e9" alt=""><figcaption><p>Analysis results — figures, insights, next step recommendations</p></figcaption></figure>
{% endstep %}
{% endstepper %}

The more analyses you run within a analysis chat, the more context the AI accumulates, enabling increasingly deeper insights.

### **3.2. Stopping an analysis**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FwNrAN3LnPWJEoD1pQvBU%2Fimage.png?alt=media&amp;token=04566868-3f3c-41a7-8aac-969aa95bcc48" alt=""><figcaption><p>The [Stop] button shown while an OmicsHorizon AI is running</p></figcaption></figure>

* If a prompt was entered incorrectly or the analysis is heading in an unintended direction, click the \[Stop] button on the right side of the chat input field to stop the running analysis immediately.
* While an analysis is running, the send button changes to a \[Stop] button.
* All steps in progress are stopped together, and you can continue by entering a new prompt afterward.

***

## 4. Reviewing Analysis Assets

In the **Analysis asset** panel on the left side of the analysis screen, you can view all outputs generated in the current analysis.

### 4.1. Analysis data

Files generated by the AI — such as figures and CSV files — are organized by analysis run. The most recent results appear at the top. Each file can be downloaded individually.

### 4.2. Added files

The list of files you have uploaded to the current analysis. Each file can be downloaded or saved to the library.

### 4.3. Workflow

The list of workflows added to the current analysis. Select a workflow from the list to apply it to the next chat input.

### **4.4. Merge as new workflow**

You can merge your analysis history so far into a single workflow and save it to the library.

{% stepper %}
{% step %}
**Click the \[Merge as new workflow] button.**
{% endstep %}

{% step %}
**Click \[Confirm] in the confirmation modal.**

The AI processes the merge automatically. The merged workflow is saved to the library upon completion.
{% endstep %}
{% endstepper %}

***

## 5. Managing Analyses

### 5.1. Renaming an Analysis

Click the analysis name at the top of the screen, or go to **\[More ⋯] → \[Rename analysis]** to edit the name. It saves automatically when you move focus away.

### 5.2. Adding to Favorites

Go to **\[More ⋯] → \[Favorite]** to pin the analysis to your favorites in the left sidebar for quick access.

### 5.3. Deleting an Analysis

Go to **\[More ⋯] → \[Delete]** to open the analysis deletion modal.

{% hint style="info" %}

* Deleting an analysis **permanently removes all chat history, analysis result files, and Studio outputs** associated with it. Deleted data cannot be recovered.
* You must type the exact name of the analysis to confirm deletion.\
  Files saved separately to the library are not affected. {% endhint %}
  {% endhint %}

***

## 6. Studio

Automatically generate papers, presentations, and reports from your analysis results.

**Because the AI performed the entire analysis itself, you can produce publication-ready outputs with a single click.**

{% hint style="info" %}
Studio features are only activated when analysis results are available.\
Run an analysis first, then use Studio.
{% endhint %}

### 6.1. Report

Collects all key results from the analysis and generates a comprehensive report including figures, tables, and statistical results.

{% stepper %}
{% step %}
**Select the \[Report] panel in Studio.**
{% endstep %}

{% step %}
**Click \[Generate].**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FRock6vHgKohRzOi3PFZ1%2Fimage.png?alt=media&amp;token=cfa9bbfc-7e10-464a-95bc-a87d7baf9494" alt=""><figcaption><p>Report generation result</p></figcaption></figure>
{% endstep %}
{% endstepper %}

### 6.2. Paper method

Writes a publication-ready Methods section based on the exact analysis steps the AI performed.

{% stepper %}
{% step %}
**Select the \[Paper method] panel in Studio.**
{% endstep %}

{% step %}
**Click \[Generate].**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FowrtNRPyWUzxdm7mm7sO%2Fimage.png?alt=media&amp;token=892409c4-438c-4b00-85d1-58447273e180" alt=""><figcaption><p>Paper method generation result</p></figcaption></figure>
{% endstep %}
{% endstepper %}

{% hint style="success" %}
Because the draft is based on every step the AI actually performed, it significantly reduces the omissions and errors that occur when writing Methods manually.
{% endhint %}

### 6.3. Slides

Summarizes the analysis conversation and extracts key findings to generate presentation slides.

{% stepper %}
{% step %}
**Select the \[Slides] panel in Studio.**
{% endstep %}

{% step %}
**Click \[Generate].**

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FrIXQ3EP60q1S1pwi2Iag%2Fimage.png?alt=media&amp;token=71bed771-0fec-466e-8e5f-04f284d8f6a7" alt=""><figcaption><p>Slides generation result</p></figcaption></figure>
{% endstep %}
{% endstepper %}

### 6.4. Paper

The AI automatically searches for the latest papers related to your analysis.

{% stepper %}
{% step %}
**Select the \[Paper] panel in Studio.**
{% endstep %}

{% step %}
**Click \[Generate].**

The AI extracts disease terms, analysis methods, and biological keywords from the conversation to search for related papers.
{% endstep %}

{% step %}
**Review the list of related papers.**

Click \[View paper] next to any paper to open it in a new tab.

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2F9pTEu2r4LCed8f2CqYn3%2Fimage.png?alt=media&amp;token=0f0d56a7-7f1f-4bd2-816f-3f969c8603bb" alt=""><figcaption><p>Related paper search results</p></figcaption></figure>
{% endstep %}
{% endstepper %}