DoseRider
Enhancing Toxicogenomics with Advanced Dose-Response Analysis at the Pathway Level
About DoseRider
DoseRider advances toxicogenomics by applying mixed models with cubic splines to analyze nonlinear dose-response relationships at the pathway level. This approach supports multi-omics research, making it accessible both as an R package and a web application. It identifies trends across pathways and features (such as proteins, genes, and metabolites) and calculates trend change doses (TCD) and benchmark doses (BMD). DoseRider reveals critical dose-response patterns and molecular insights, enhancing the understanding of how compounds or drugs affect biological systems at various doses.
Explore pre-analyzed multi-omics datasets
Explore and visualize dose-response relationships using DoseRider with pre-analyzed public datasets. DoseRider leverages Generalized Linear Mixed Models (GLMMs) to examine pathway responses, offering insights into significant pathways and variability across features such as proteins, genes, and metabolites.
Click "View Results" to visualize the outcomes from existing studies, or click "Run Analysis" to perform your own analysis using custom parameters.
For more information on the analysis, visit the FAQ section.
| Project ID | Chemical | Dose | Time point | Species | Omic type | Annotation | Results | New analysis |
|---|---|---|---|---|---|---|---|---|
| PRJNA869442 | 2,4-BPF | 0,5.00e-04,1.00e-03,1.00e-02,1.00e-01,5.00e-01,1.00e+00,5.00e+00,1.00e+01 µM | Homo sapiens | RNA-seq | symbols | View Results | Run analysis | |
| PRJNA869442 | 2,4-BPS | 0,5.00e-04,1.00e-03,1.00e-02,1.00e-01,5.00e-01,1.00e+00,5.00e+00,1.00e+01,5.00e+01,1.00e+02 µM | Homo sapiens | RNA-seq | symbols | The dataset was not analized | Run analysis | |
| PRJNA869442 | 4,4-BPF | 0,5.00e-04,1.00e-03,1.00e-02,1.00e-01,5.00e-01,1.00e+00,5.00e+00,1.00e+01,5.00e+01 µM | Homo sapiens | RNA-seq | symbols | The dataset was not analized | Run analysis | |
| PRJNA869442 | BADGE | 0,5.00e-04,1.00e-03,1.00e-02,1.00e-01,5.00e-01,1.00e+00,5.00e+00,1.00e+01 µM | Homo sapiens | RNA-seq | symbols | The dataset was not analized | Run analysis | |
| PRJNA869442 | BPA | 0,5.00e-04,1.00e-01,5.00e-01,1.00e+00,5.00e+00,1.00e+01 µM | Homo sapiens | RNA-seq | symbols | The dataset was not analized | Run analysis |
Explore and analyze dose-response data
Upload your data to analyze dose-response relationships across features like proteins, genes, and metabolites. DoseRider applies GLMMs and cubic splines to detect both linear and nonlinear trends at the pathway level. Fill out the form below to start your analysis.
Check the required format for analysis in the FAQ section or download our test dataset.
DoseRider requires two files: an expression dataset (genes, proteins, metabolites, etc.) and a metadata file with sample information, including a "dose" column for dose-response modeling, supporting formats like CSV and Excel.
Code and Contributions
Interested in contributing to DoseRider or seeing the code? Visit our GitHub repository at https://github.com/icbi-lab/DoseRider.