Data Upload & Configuration

Try Demo Data

Load a built-in demo dataset to explore the dashboard's features.

Data must be in long format — one row per observation/measurement.

Session Save / Restore

Save your current analysis state (settings, results, plots) and reload it later to continue where you left off.

Save Session

Tumor Growth Analysis

Configure analysis parameters and run statistical modeling. Ensure data is uploaded first from the Data Upload tab.

Analysis Parameters

LME4 models tumor volume trajectories over time using a linear mixed-effects model, which handles repeated measures and unequal timepoints. AUC summarizes total tumor burden as the area under each animal's growth curve.
The group all comparisons are made against (typically a vehicle or IgG control). Automatically set to the most likely control group when data is uploaded.
Determines which group comparisons are performed after the primary model. 'vs Reference' tests each treatment against the reference group using Dunnett's correction, which is designed for this comparison structure and is less conservative than Bonferroni. 'All Comparisons' tests every pair with Tukey HSD familywise error correction.
Transformation applied to tumor volume before modeling. Log transformation is recommended for most tumor growth data as it stabilizes variance and linearizes exponential growth. Use 'None' for already-linear data.
Number of recent timepoints used to estimate the growth slope for extrapolating tumor volumes of mice that died before the study end. Set to 0 to disable. If an Event/Censor column is mapped in Data Upload it will be used; otherwise mice that disappear before the final timepoint are automatically detected.
Controls whether cage is included as a covariate to account for housing effects on tumor growth. 'Include if not collinear' adds cage automatically when it is statistically separable from treatment. Requires a Cage ID column to be mapped in Data Upload.
Specifies the random effects structure for individual animals. 'Intercept only' allows each animal to have its own baseline volume. 'Intercept + Slope' also allows individual growth rates, which is more flexible but may fail to converge with small samples.

Export All Results

Download every available result table (CSV) and plot (PNG) as a single ZIP file.

Download All Results
Download ANOVA
Per-animal exponential growth rates estimated from each subject’s individual tumor volume trajectory using linear regression on log₁ₚ(volume) vs time. Requires ≥3 time points per animal. All rate, fold change, and percent change values are on a per-day basis.
  • Treatment — treatment group.
  • ID — individual animal identifier.
  • Cage — cage identifier.
  • Growth Rate — slope of the log₁ₚ(volume)–time regression (units: log-volume per day). Represents the instantaneous exponential growth constant: a value of 0.10 means ~10% volume increase per day on a continuous compounding basis.
  • GR 95% CI Lower/Upper Bound — 95% confidence interval for the log-scale growth rate.
  • Fold Change — exp(Growth Rate): multiplicative volume change per day. A value of 1.10 means the tumor is 10% larger each day; values below 1.0 indicate regression.
  • FC 95% CI Lower/Upper Bound — exp(GR CI bounds): back-transformed confidence interval for the daily fold change.
  • Percent Change — (Fold Change − 1) × 100: daily volume change expressed as a percentage (e.g. +10.5%/day or −3.2%/day).
  • PC 95% CI Lower/Upper Bound — (exp(GR CI) − 1) × 100: back-transformed CI bounds for the percent change.
  • R² — coefficient of determination from the per-animal log-linear regression. Values close to 1.0 indicate a good exponential fit; lower values suggest irregular growth or too few time points.
These are descriptive per-animal values used to visualise within-group spread and for sample size estimation. For group-level inference, use the Treatment Effects tab.
Download Growth Rates
Descriptive statistics for tumor volume by treatment group and timepoint. Shows mean, standard deviation, and standard error across subjects measured at each study day.
  • Treatment — treatment group.
  • Day — study day (measurement timepoint).
  • Mean — mean tumor volume (mm³) for the group at that timepoint.
  • SD — standard deviation of volume across animals in the group.
  • SEM — standard error of the mean (SD / √N).
  • N — number of animals with a measurement on that day.
Useful for inspecting raw descriptive trends across time and confirming data entry. Statistical comparisons should use the ANOVA, Comparisons, or AUC Summary tabs as appropriate.
Download Data Summary

Tumor Growth Curves

Growth Rates Plot

Area Under the Curve Plot

Waterfall Plot

Effect Size Forest Plot

Q-Q Plot of Residuals

Residuals vs Fitted

Survival Analysis

Analyze time-to-event data using Kaplan-Meier survival curves and proportional hazards models. Ensure data is uploaded and configured in the Data Upload tab.

Analysis Parameters


Survival summary: Per-group event counts, total subjects, event rate, and median survival time (the day by which 50 % of animals have reached the endpoint). ‘Not reached’ means fewer than half the group experienced an event by the end of the study.
Cox proportional hazards model. Hazard Ratios (HR) are computed relative to the reference group. Firth’s bias-reduced method is applied automatically when a group has zero events.
  • Group — treatment group name.
  • HR — Hazard Ratio: the instantaneous risk of the event in this group relative to the reference. HR < 1 means lower hazard (better survival); HR > 1 means higher hazard.
  • CI_Lower / CI_Upper — 95 % confidence interval for the HR. If this interval does not include 1.0, the difference is statistically significant at the 5 % level.
  • P_Value — p-value for the individual group coefficient from the Cox model.
  • Events — number of animals that experienced the endpoint (e.g. reached the tumour size threshold or were euthanised).
  • Total — total number of animals in the group.
  • Event_Rate — Events ÷ Total. Values close to 1.0 mean most animals reached the endpoint.
  • Median_Survival — day by which 50 % of the group experienced the event. ‘Not reached’ if fewer than half had events by study end.
  • Note — flags the reference group row.
Download Results

Group colours are mapped automatically from the analysis groups.

Annotation

Kaplan-Meier Survival Curves

Hazard Ratio Forest Plot

Numbers at risk table: one row per group per event time point, summarising what happened to the cohort at that moment.
  • Group — treatment group name.
  • Time — the day on which one or more events occurred.
  • N_Risk — number of animals still alive and uncensored at the start of this time interval.
  • N_Events — number of animals that experienced the endpoint at exactly this time.
  • N_Censored — number of animals whose last observation was at this time without experiencing the endpoint (e.g. removed from study).
  • Survival — Kaplan–Meier estimated survival probability at this time point (1.0 = 100 % surviving).
N_Risk decreases over time as events and censoring accumulate; a rapid drop indicates many events in a short window.
Download Table

Analysis Log

Events logged during your session (data uploads, analysis runs, errors). Logs are stored in memory and cleared when the session ends.
Download log 

              

            

          

        

        

          

            
Help & Documentation

            

              

                
                 Disclaimer
              

              

                mouseExperiment
                 is provided "as is" for research purposes only,
                 without warranty of any kind, express or implied. The authors and contributors
                 accept no liability for errors, inaccuracies, or any consequences — including
                 but not limited to incorrect results, data loss, or decisions made on the basis
                 of outputs from this software.
                 All results must be independently validated before use in publications, reports,
                 regulatory submissions, clinical decisions, or any other application.
              

            

            

            

              

                

                  

                    
                     Documentation
                  

                  

                    Full documentation, tutorials, and function reference for the 
                    mouseExperiment
                     package:
                  

                  
                    
                     GitHub Repository
                  
                

              

              

                

                  

                    
                     Report Issues
                  

                  
Found a bug or want to request a new feature? Open an issue on GitHub:

                  
                    
                     Submit Issue / Feature Request
                  
                

              

            

            

            
Column Naming

            
The dashboard looks for common column names like:

            
    
              
  • 
                ID:
                ID, Mouse_ID, Animal_ID, Subject
              
    • 
              
  • 
                Time:
                Day, Time, Timepoint
              
    • 
              
  • 
                Volume:
                Volume, Tumor_Volume
              
    • 
              
  • 
                Treatment:
                Treatment, Group
              
    • 
              
  • 
                Cage:
                Cage, Cage_ID
              
    • 
              
  • 
                Dose (optional):
                Dose, dose, DoseLevel
              
    • 
              
  • 
                Survival/Censor (optional):
                Survival_Censor, Censor, Event — numeric column coded as 
                1 = event (e.g. death)
                 and 
                0 = censored
                .
              
    • 
            

            
Statistical Methods

            
The analysis uses linear mixed-effects models (lme4) or area under the curve (AUC) methods.

            

              Consult the 
              mouseExperiment documentation
               for detailed method information.
            

            
Troubleshooting

            

              File won't upload:
              Ensure it is a CSV or RDA file.
            

            

              Columns not detected:
              Check that column names match expected patterns above.
            

            

              Analysis tab greyed out:
              Upload and configure data first. Survival requires a censor column; Dose Response requires a dose column; Drug Synergy requires at least 3 treatment groups (e.g. control, Drug A, and combination).
            

            

              Analysis fails:
              Check that required columns are selected and contain valid data.
            

          

        

        

          

            
About

            

              

                

                  

                    
                     mouseExperiment
                  

                  

                    
                      

                        
                          Version
                        
                        0.1.0
                      

                      

                        
                          Last Updated
                        
                        2026-03-25
                      

                      

                        
                          Repository
                        
                        
                          github.com/sciOmics/mouseExperiment
                        
                      

                    
                  

                

              

              

                

                  

                    
                     mouseExperimentDashboard
                  

                  

                    
                      

                        
                          Version
                        
                        0.1.0
                      

                      

                        
                          Last Updated
                        
                        2026-03-25
                      

                      

                        
                          Repository
                        
                        
                          github.com/sciOmics/mouseExperimentDashboard
                        
                      

                    
                  

                

              

            

            

              
How to Cite

              
If you use mouseExperiment or this dashboard in your research, please cite:

              

                

                  mouseExperiment: 
                  An R package for statistical analysis of mouse tumor growth experiments.
                

                

                  Available at: 
                  https://github.com/sciOmics/mouseExperiment
                

              

            

            

              
R Citation

              
To get the citation information directly in R:

              
citation("mouseExperiment")

            

            

              
License

              

                mouseExperiment is released under the 
                MIT License
                .