Getting Started with BioRender Graphing

Note: The new BioRender Graphing is currently in limited availability, Early Access to select customers. For information on the current BioRender Graph experience, click here.

BioRender Graphing is BioRender's new statistical graphing and analysis tool. It brings together data import, graph creation, outlier detection, and statistical analysis in one unified workflow. This article covers the full end-to-end experience - from importing your data to running and interpreting analyses.

Overview

When BioRender Graphing is enabled on your account, you'll see it marked as “Graphing” in the left-hand toolbar in the new BioRender canvas. BioRender Graphing files will show as a Green graphing icon on your illustration. Legacy Graph files will appear grayed in your Gallery.

Each BioRender Graphing file is organized into three tabs:

1. Data -  Import and manage your datasets
2. Graph - Create, view, and customize graphs
3. Analysis - Run and review statistical analyses

Step 1: Enter your data

There are two ways to get data into a BioRender Graphing file.

1. Upload a file (Smart Data Import)
2. Blank Spreadsheet

Option 1: Upload a file (Smart Data Import)

1. On the Data tab, click Upload dataset.
2. Select your Excel, CSV, or .prism file.
   • Files with multiple sheets will show all available sheets - select all or choose one.
   • For .prism files, the option to import graphs and analyses is turned on by default. If you only want the raw data, uncheck this option.

3. Click Import to confirm.

4. Review the auto-detected variables in the import preview.

5. Edit variable names or assignments if needed.

💡 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

Option 2: Blank spreadsheet (Coming soon)

1. Click the Blank spreadsheet on the Data tab.
2. Paste your data directly into the spreadsheet
3. Click Detect variables to run the Smart Data Import logic on your data.

How datasets are organized

Once imported, each dataset appears as a tab along the bottom of the Data tab.  You can click between datasets to view them. Variables for the active dataset are listed in the left panel.

From the data view, you can:

• Manually add or delete variables
• Rename variables
• See which graphs are linked to each dataset

Step 2: Create a graph

Creating your first graph

1. From a dataset on the Data tab, click Create new graph.
2. This takes you to the Graph editing page.
3. Select your graph type (e.g., bar chart, column chart, scatter plot, mean/median line).
4. Assign your variables - the graph preview updates in real time as you fill in each field.
5. Once the preview looks right, click Continue.

Customizing your graph

After clicking Continue, the customization panel opens on the right side of the screen. 

Settings are organized into sections:

Display data (shown first — this is the most commonly needed setting)

• Choose what to plot: mean with standard deviation, mean with SEM, etc.
• Toggle Show individual data points on or off — this option has been moved to a prominent position at the top of the panel, since it was frequently hard for users to find in legacy Graph.

Color and font

• Adjust graph colors, font styles, and sizes.

Additional settings

• Access more advanced options for axis formatting, spacing, and lines.

Tip: You must confirm or save your graph details before you can run a new statistical analysis. If the Run Analysis button appears unresponsive, check whether the graph details panel is still open in edit mode - close or confirm it first. 

Editing graph details after your graph creation

Graph details (type, variables, dataset) can be reopened and edited at any time. When you re-open graph details in edit mode, a prompt will ask 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. 

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.

Tip: 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:

• Exclude individual data points: Right click any data point - including non-outliers - to manually exclude it. 
• 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.

Step 4: Run a statistical analysis

Starting an analysis

1. On the Graph editing page, click Run analysis.
2. A structured form appears with three sections:

Section 1 - Analysis type 

When possible, BioRender Graphing 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 (e.g., choosing a parametric test when the data isn't normal), A warning recommendation will explain 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 out 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. 

Example (based on a one-way ANOVA) 

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 will 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.

Example (based on a one-way ANOVA)

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.

Example (based on a one-way ANOVA) 

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 Analysis 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 (e.g., switching from a bar chart to a box plot, or adjusting one variable)
• Delete

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. On the Data tab, click Upload dataset and select your .prism file.
2. All datasets from the file will appear - select all or choose specific ones.
3. The option to import graphs and analyses is turned on by default. If you only want the raw data, uncheck this option.
4. Click Import.

What gets imported

• All selected datasets appear as tabs on the Data tab, with associated graphs shown.
• In the Graph Grid View, imported graphs are clearly marked with a Prism import badge.
• In the Analysis tab, imported analyses appear with their results attached, and any significant markers are automatically applied to the corresponding graph.
• You can interact with imported analyses just like ones you've run yourself - toggle results on/off, adjust settings, or run new analyses on top of them.

Known limitations

• Styling is not preserved. Prism graph customization (colors, fonts, formatting) cannot be extracted from the Prism file. BioRender will recreate the graph type as best it can based on the data, and you can restyle from there.
• Some analysis outputs may not be available. For example, 95% confidence intervals on a dose-response curve may not be recreatable from the Prism file alone. In these cases, the option will appear grayed out with a tooltip instructing you to run a new analysis in BioRender to generate it.
• Prism import works well for common graph types like bar charts and ANOVAs. More complex curve fits may require re-running the analysis in BioRender.

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 (coming soon) - Select one or more graphs and use Add to illustration to push them to an existing illustration file. A modal will let you choose which file to send them to.

Need help or have feedback? 

Contact our Support team at support@biorender.com or reach out by clicking on the "Help" bubble in the right hand corner in the app.