Omics
analysis,
open to all

Get an instant overview of your dataset: sample count, feature distribution, missing value patterns visualised as an interactive heatmap, coefficient of variation per feature, and class balance. An outlier detection module using Isolation Forest flags suspicious samples before any downstream analysis.

A complete, ordered pipeline: filter by missing-value threshold, impute with KNN or median, normalize (log₂, Z-score, quantile, robust), correct batch effects with ComBat, apply variance filtering, and validate the result in a post-QC dashboard — all in a single step with data-driven auto-suggestions.

Every plot is fully interactive (Plotly) — zoom, pan, hover tooltips, lasso selection, publication-ready export at 2× resolution. Dimensionality reduction, clustering heatmaps, signal profiles and pairwise comparisons all in one module.

Multi-group and pairwise statistical comparisons with FDR-corrected p-values. The volcano plot supports multi-class mode, customisable fold-change and p-value thresholds, and direct export of significant features into enrichment. UpSet & Venn plots reveal exclusive and shared features across conditions.

Train and evaluate machine learning and deep learning models for classification or continuous regression (new in v1.2). Full pipeline: cross-validation, hyperparameter tuning, confusion matrices, ROC curves, R² and RMSE metrics — plus explainability via SHAP & LIME at sample and global level. Models are exportable as .pkl for real-time inference.

GSEA is new in v1.2, joining the existing Over-Representation Analysis. Both methods run across 100+ databases via gseapy. The smart auto-detection engine pre-fills the feature input from any upstream result: click a heatmap cluster, a volcano significant set, a Venn exclusive zone — or paste manually.

Model time-to-event outcomes from omics features. Kaplan–Meier estimator with log-rank test, Cox proportional hazards regression with forest plot, and risk group stratification. All curves are interactive and publication-ready.

A dedicated module for repeated-measures and time-series omics data. Load a dataset with Subject_ID and Time columns and instantly visualise molecular trajectories, compare group dynamics, and run time-point statistics.

At any point in your session, generate a complete, self-contained HTML report capturing every analysis: all interactive Plotly figures, statistical tables, model metrics, enrichment results and a table of contents. The file opens in any browser with no dependencies — shareable, archivable, publication-ready.

Run the complete Profiler platform locally — no internet, no account, no upload size limit. MSI2Profiler is a companion desktop tool for preprocessing Mass Spectrometry Imaging data (.imzML), defining ROIs and exporting matrices directly importable into Profiler.