HiMaLAYAS Documentation

Hierarchical Matrix Layout and Annotation Software (HiMaLAYAS) is a framework for post hoc enrichment-based annotation of hierarchically clustered matrices. It treats dendrogram-defined clusters as statistical units, tests annotation enrichment, and renders significant annotations alongside the matrix. HiMaLAYAS supports biological and non-biological domains.

This documentation walks through installation, workflows, and examples using HiMaLAYAS.

Start Here

• Introduction
• Installation

Notebook Walkthrough

• Quickstart Notebook (HTML)
• Run Quickstart in Binder

Core Workflow

1. Load a real-valued matrix into Matrix.
2. Load term-to-label annotations into Annotations.
3. Run Analysis.cluster() and Analysis.enrich().
4. Call Analysis.finalize() to attach layout and Benjamini-Hochberg FDR-adjusted q-values.
5. Plot with Plotter and summarize clusters.

Use Cases

• Annotate clustered matrices for biological or non-biological data.
• Zoom into a cluster and rerun enrichment on the subset.

Citation

For a full description of HiMaLAYAS and its applications, see:

Horecka, I., and Röst, H. (2026)
HiMaLAYAS: enrichment-based annotation of hierarchically clustered matrices
bioRxiv. https://doi.org/10.64898/2026.02.11.705303
Submitted to Bioinformatics.