> 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/integrative-analysis.md).

# Integrative Analysis

Connect results from multiple analyses into a single research narrative.

**Patterns invisible in individual analyses emerge through Integrative Analysis.**\
Based on the selected analysis conversations within the project, insights are generated by comprehensively analyzing the similarities, differences, and causal relationships across analyses to provide a broader understanding of the overall research.

{% hint style="info" %}
It allows when two or more analyses have been completed within the project.
{% endhint %}

<figure><img src="https://752667642-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjSFvZPRsEeeEZdRHxLlX%2Fuploads%2FZQdj2dCqxeCIyYUwOFwY%2Fimage.png?alt=media&amp;token=b9d55a22-8a0b-4654-8a01-9cd1acf8138b" alt=""><figcaption><p>Integrative analysis screen</p></figcaption></figure>

***

## 1. Insight Synthesis

Add the analyses you want to synthesize as Context, enter your research intent, and the AI identifies shared patterns and key insights across the selected analyses.

{% stepper %}
{% step %}
**Click \[Add Context] above the chat input and select your analyses.**

1. Choose the analyses you want to compare or synthesize from the project list.
2. You can add up to **5 analyses**.
3. The insights generated depend on which analyses you select. Choose analyses that align with the specific question you're trying to answer.
   {% endstep %}

{% step %}
**Enter your intent in the chat input.**

Just like in AI Data Analysis, type your research intent in natural language.

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

* "Find common patterns related to immunotherapy response across the 4 selected analyses."
* "Summarize microbiome features that consistently differ between responders and non-responders across the selected analyses."
  {% endhint %}
  {% endstep %}

{% step %}
**Review the AI-generated integrated insights.**

The AI connects findings across the selected analyses and presents a unified research narrative.
{% endstep %}

{% step %}
**Review the recommended next steps.**

1. Alongside the integrated insights, the AI suggests specific follow-up analyses to consider.
2. Each recommendation can be launched with a single click.
   {% endstep %}
   {% endstepper %}

{% hint style="success" %}
Changing the Context combination surfaces different angles of insight.\
Try running Insight Synthesis multiple times with different selections to explore your project from multiple perspectives.
{% endhint %}

***

## 2. 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.

### 2.1. 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.**
{% 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 %}

### 2.2. 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 %}

***

## 3. 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.

### 3.1. Analysis data

Files generated by the AI — such as figures and CSV files — are organized by analysis run. Each file can be downloaded individually.

### 3.2. Added files

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

***

## 4. Managing Analyses

### 4.1. 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.

### 4.2. Adding to Favorites

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

### 4.3. Deleting an Analysis

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

{% hint style="warning" %}

* Deleting an analysis **permanently removes all chat history, analysis result files, and Studio outputs** associated with it.&#x20;
  * Deleted data cannot be recovered.
  * Files saved separately to the library are not affected.
* You must type the exact name of the analysis to confirm deletion.
  {% endhint %}

***

## 5. 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 %}

### 5.1. 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%2F39c2GVZyJFgVKNT7qItQ%2Fimage.png?alt=media&amp;token=f0d778b1-aa6d-4d32-98e1-ceb5d117047c" alt=""><figcaption><p>Report generation result</p></figcaption></figure>
{% endstep %}
{% endstepper %}

### 5.2. 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%2FqLgjDEiOE2yl1lOdisSK%2Fimage.png?alt=media&amp;token=9abd35ae-045b-4cf4-a8c8-a0caaf0eea93" alt=""><figcaption><p>Report 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 %}

### 5.3. 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%2FrzqQaSLpThWPzcSrXWUv%2Fimage.png?alt=media&amp;token=9c295c2c-3d7d-4106-8911-1c496fb0515d" alt=""><figcaption><p>Slides generation result</p></figcaption></figure>
{% endstep %}
{% endstepper %}

### 5.4. 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%2FM2ObVJbJV4VTtTmxBeCr%2Fimage.png?alt=media&amp;token=d31f6d39-7fb2-41ea-9613-6ae1804465af" alt=""><figcaption><p>Related paper search results</p></figcaption></figure>
{% endstep %}
{% endstepper %}