Getting Started with BioRender Graphing

BioRender Graphing is BioRender's statistical graphing and analysis tool. The Graphing agent takes you from raw data to a publication-quality graph in minutes, and you can edit manually at any point in the process. It brings together data import, graph creation, outlier detection, and statistical analysis in one workflow, so there's no manual data prep, no new tool to learn, and no tool switching.

You can also create multiple graphs from the same dataset without restructuring your data, use built-in pre-tests that recommend the right statistical test and explain why, and import your existing Prism files. Everything is stored securely in BioRender.

📌 Beta: Graphing agent is currently in beta. 

In this article, you'll learn how to:

• Create a Graphing file
• Add your data
• Create a graph with the BioRender AI agent
• Review outliers and run a statistical analysis
• Customize your graph
• Manage multiple graphs, match styles, and export your work
• Use Style Match
• Export your graphs and analysis

Create a BioRender Graphing file

From your Gallery:

1. Click “Create New” in the upper left corner.
2. Select “Graph”.
3. Click “New Graphing”.

How a Graphing file is organized

Tabs at the top: “Data”, “Graph”, and “Analysis”.

• “Data”: import and manage your datasets
• “Graph”: create, view, and customize graphs
• “Analysis”: run and review statistical analyses
• BioRender AI agent: the “Ask BioRender” chat box. 

Click it to open the conversation. The agent stays available on all three tabs and keeps your conversation and data when you switch tabs, so you never need to restart or re-upload.

Step 1: Add your data

1. Open your new Graphing file. The agent greets you and explains what it can do: help you upload a spreadsheet, build graphs, and run analyses.
2. Click “Upload data” in the agent's message, or click the “+” button in the chat box. Both start the same import. At any point, you can add more data this way.
3. Choose your file. Supported formats: .csv, .xls, .xlsx, .prism, and .pzfx (up to 50 MB). 
4. In the “Select datasets from your file” window, review the datasets the agent found. Each one shows its number of rows and columns.
5. Select the datasets you want, or choose “Select All”, then click “Import data”.
6. The agent confirms what it added. It then describes what it sees, highlights the variables it detected, and suggests a graph type.

Other ways to start from an empty file manually

1. Blank spreadsheet: paste or type in your own data. When you're done, click “Re-detect variables”.
2. Try a sample dataset: explore with ready-made example data.
3. Add dataset (top right): add another dataset at any time. 

💡 Importing from GraphPad Prism? BioRender supports .prism files (newest format). Older .pzfx files will import data only. See the full guide: Importing from GraphPad Prism. 

For full steps and data limits, see How to add your data in BioRender Graphing.

Step 2: Create a graph

With the BioRender AI agent 

1. Once your data is in, the agent recommends a graph type. You can also ask for one yourself. For example: "Help me set up a graph from [dataset name]."
2. The agent suggests a graph type that fits your data and asks you to confirm. Confirm your graph type or request a different graph.
3. The agent tells you what that graph needs (for example, a numeric X-axis and a numeric Y-axis) and assigns your variables.
4. The agent shows a plan that summarizes the graph. Click “Create the graph”.
5. The agent will help navigate you around the UI automatically, as well as provide clickable interactions to take you there.
6. The agent suggests a next step, such as fitting an analysis to compare cell lines. Confirm, or ask it to action something else.
7. Edit the graph through the agent.
8. Undo edits in one click or request the agent undo the action.

Example: Creating a Dose response curve with the Graphing agent (with chat in the side panel).

💡 Tips for good prompts

• Name the dataset, variables, or groups you are working with. The agent works from the variables BioRender detected.
• If the agent isn't sure which variable or group you mean, it will clarify. Answer in plain language, or click its suggestions.
• If a suggestion isn't right, say what you want instead.
• If the agent can't do something, it tells you what it couldn't complete. Try rephrasing, or use the manual steps below.

Manual option

1. On the Data tab, open the “Graphs” panel on the right. Search or browse graph types.
2. Click the graph you want to create. This takes you to the Graph editing page.
3. In the Graph details panel, assign your variables. The graph preview updates in real time as you fill in each field.
4. Once the preview looks right, click “Continue”.

Explore the Graph page

• Graph details (left): your dataset, variables, and grouping. Click “Edit” to change them.
• Analysis (left): click “Run new analysis”. Your reports appear below. An outlier analysis (ROUT) runs automatically.
• Toolbar (top): “Resize graph”, “Style match”, and “Comment”.
• Customize graph (top right): opens the Customize graph panel.
• Displayed data (below the graph): the data behind what you see.
• “Ask BioRender” (bottom center): click to keep working with the agent.

💡 You must confirm or save your graph details before you can run a new statistical analysis or customize your graph. If “Run new analysis” seems unresponsive, check whether the Graph details panel is still open in edit mode. If it is, close or confirm it first.

Editing graph details later

Graph details (type, variables, dataset) can be reopened with “Edit” at any time. When you reopen graph details in edit mode, a prompt asks if you want to keep or discard any unsaved edits before confirming changes.

Step 3: Review outlier detection

Outlier detection runs automatically on every graph. You don't need to trigger it manually. BioRender uses the ROUT (Robust regression and Outlier removal) method for outlier detection. 

You can also ask the agent to add the outlier detection to your graph.

What you'll see

• The number of detected outliers appears in the left panel.
• Outliers are automatically detected and highlighted in the data table beneath the graph.
• Click the outlier report to open the full outlier report, which shows:
  • Total number of data points analyzed
  • Number of outliers detected
  • A breakdown of outliers by group

Adjusting sensitivity with the Q parameter

If you want to change how aggressively outliers are identified, you can adjust the Q parameter:

1. Open the outlier report.
2. Click “Update settings”.
3. Enter a Q value between 0.1 and 10:
   • Lower values = stricter (fewer outliers flagged)
   • Higher values = more lenient (more outliers flagged)
4. Click “Rerun” to apply the updated threshold and see revised results.

💡 This is useful when you want to test how borderline a given outlier is, for example to confirm whether a data point is a definitive outlier or just on the edge.

Excluding data points

You have two options for handling outliers and other data points you want to exclude:

1. “Exclude individual data points”: Right-click any data point, including non-outliers, to manually exclude it.
2. “Exclude all detected outliers at once”: Use the “Exclude all outliers” checkbox in the outlier report to toggle all outliers in or out in one click. Turn this on or off to compare results.

For more information, see Understanding outlier detection (ROUT method).

Step 4: Customize your graph

With the BioRender AI agent: Click “Ask BioRender” and describe the change. For example:

• "Make the colors grayscale, except keep compound B in red."
• "Change all data points to diamond shapes."
• "Make all the data points black that are less than y = 2 or greater than y = 98."
• "Color red the data points in Compound B that are between 9.899 and 103.1 on the x-axis."

Your underlying data stays unchanged. The agent makes changes with the same Graphing tools in BioRender, so your graph stays fully editable by hand. You can undo a change with the undo arrow in the upper left corner or ask the agent to undo the action. 

Manually: Click “Customize graph” in the upper right corner of the Graph tab. In the Customize graph panel:

• Display data: choose how data is plotted.
• Appearance: set the color theme, font, and color.
• Additional settings: turn the graph title, axis titles, axis labels, and legend on or off.

To edit a specific part of your graph, click it directly: the data, an axis, the legend, or a title and use the "Customize Graph" tab.

For prompts, tips, and every manual option, see How to customize your graph.

Step 5: Run a statistical analysis

With the BioRender AI agent

1. In the chat, type "run an analysis," or name the analysis you want.
2. The agent lists the analyses available for your graph type. 
3. Click a suggestion, or type the one you want.
4. Follow the agent's prompts to set up the analysis. 
5. Review your results in the “Analysis” tab and make any final adjustments in the structured form.. 
6. Then click on “Run Analysis”.

💡 The analyses available depends on your graph type. The agent only runs analyses that Graphing supports.

Manually

1. On the Graph page, click “Run new analysis”.
2. A structured form appears with three sections.

Section 1: Analysis type

When possible, BioRender Graphing's analysis guidance automatically recommends the most appropriate statistical test based on your data. The recommended test is marked with a badge.

• You can override the recommendation by opening the dropdown to see all available options.
• If you select a test that doesn't match your data's assumptions (for example, choosing a parametric test when the data isn't normal), a warning explains why the recommended test is still preferable.
• Some tests may appear grayed out if your data doesn't meet the requirements. To understand why, check the tooltip.

Select categorical groups

• By default, all groups from the graph are included.
• Deselect any groups you don't want to include in this particular analysis.

Section 2: Fine-tune your analysis

This section allows you to adjust statistical settings for your analysis. The available options may vary depending on the type of analysis you select. BioRender will recommend settings based on pre-tests run on your data, but you can modify them if needed.

• Data setup: Define how your data is organized for analysis. The available options depend on your selected method.
• Advanced options: Expand this section to access additional configuration settings, if available.
• Assumptions: Some analyses include configurable assumptions about your data. Where applicable, you can review and adjust these settings.

Section 3: Options and additional settings

Some analyses include additional options that let you refine how results are compared and calculated. These settings are only shown when relevant to your selected analysis, and recommended options are automatically applied.

• Comparisons: Where applicable, choose how groups or conditions are compared. This may include comparing all groups or selecting specific comparisons.
• Follow-up test: Some analyses include optional follow-up tests to explore differences between groups. You can select a method or use the recommended option.
• Automatic recommendations: BioRender will suggest appropriate settings based on your analysis type and data, but you can adjust them if needed.

Viewing results

Once the analysis runs:

• A full results table and descriptive statistics appear in the Analysis panel.
• Significant comparisons are automatically added to the graph with significance markers.
• Use the checkboxes in the Graph panel to toggle which results show on the graph.
• You can run multiple analyses on the same graph and control which ones are displayed.

Managing multiple graphs: Graph Grid View

As your file grows, use the “Graph Grid View” (Graph tab) to see all graphs in the file at a glance.

Navigating the view

• Search for a graph by name
• Filter by dataset to narrow down to graphs from a specific data table
• Sort by name, created date, or last modified

Note: Graph Grid View shows only the graphs within the current file. Graphs from other files will not appear here.

Bulk actions

Select one or more graphs to access bulk actions:

• “Duplicate”: Useful for creating a variation of an existing graph (for example, switching from a bar chart to a box plot, or adjusting one variable).
• “Style match”: Copy the style of one graph and apply it to others (see below).
• “Delete”.

Style match 

Make visually consistent graphs using “Style Match” with just a few clicks: fonts, colors, axis formatting, spacing, and more. You can apply a style entirely from the Graph Grid View without opening individual graphs.

How to use it

1. Select the graph whose style you want to copy from the Graph Grid View or in your individual graph.
2. Click “Style match” > “Copy style”.
3. Select one or more target graphs.
4. Click “Paste style”.
5. The selected graphs will match the style of your initial chosen graph.

When you copy a style, you can choose which categories to apply:

• Graph styling: (checked by default): Colors, spacing, lines, fonts
• Statistics markings: (checked by default): Pairwise comparisons, best-fit lines
• Graph size and dimensions: Useful for consistent panel figures
• Axis range and scale: Useful if you've set a log scale or custom tick spacing

For a full walkthrough, see How to copy the style of a graph using Style Match in BioRender Graphing.

Exporting your graph and analyses

How to export your graph

1. Open the graph you want to export in the “Graph” tab. Make sure you are in the right tab (Data, Graph, or Analysis). Your export will download the tab you select.
2. Click the blue “Export” button at the top right of your BioRender page.
3. Select your preferred file type and resolution.
4. Click “Export” to download your graph.

How to export your analyses

1. Open the analysis you want to export in the “Analysis” tab.
2. Click the blue “Export” button at the top right of your BioRender page.
3. Select the analysis you'd like to export.
4. Click “Export” to download your analysis as a .CSV file or PDF file.

❗ Important: If you need to edit your graph in another application, export it as an SVG file. You can then edit it in vector editing tools such as Adobe Illustrator and Affinity Designer.

Importing from GraphPad Prism

If you have existing Prism files, you can import them directly into BioRender Graphing, including the data, graphs, and analyses.

Supported file format

• BioRender supports the .prism file format (the newest Prism format).
• Older .pzfx files are partially supported. Data will import, but graphs and analyses will not.
• To import a .pzfx file with graphs and analyses intact, re-save it as a .prism file in GraphPad Prism first, then import.

How to import

1. In your Graphing file, click “Upload data” ( or “+” in the BioRender AI agent chat) and select your .prism file.
2. All datasets from the file appear. Select all or choose specific ones.
3. Importing graphs and analyses is turned on by default. If you only want the raw data, uncheck this option.
4. Click “Import data”.

For more information, see How to import your Prism files into BioRender Graphing.

Adding graphs to an illustration

You can use BioRender Graphing files directly in your BioRender illustration files.

1. From the illustration editor: Use the graph insert panel within the editor to browse and insert graphs from your BioRender Graphing files. Once on the canvas, click individual graph elements to style them inline.
2. From the Graph Grid View: Select one or more graphs and use Add to illustration to push them to an existing illustration file. A window lets you choose which file to send them to.

Need help? Reach out to our support team at support@biorender.com or start a live chat by clicking the "Chat With Us" bubble in the bottom right corner.