Hierarchical Matrix Layout and Annotation Software (HiMaLAYAS) is a framework for post hoc enrichment-based annotation of hierarchically clustered matrices. HiMaLAYAS treats dendrogram-defined clusters as statistical units, evaluates annotation enrichment, and renders significant annotations alongside the matrix. HiMaLAYAS supports both biological and non-biological domains.
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://www.biorxiv.org/content/10.64898/2026.02.11.705303v2
Submitted to Bioinformatics Advances.
- Full Documentation: himalayas-base.github.io/himalayas-docs
- Try in Browser (Binder):
- Quickstart:
- Advanced Quickstart:
- Quickstart:
- Documentation Repository: github.com/himalayas-base/himalayas-docs
HiMaLAYAS is compatible with Python 3.8 or later and runs on major operating systems.
pip install himalayas
# Optional: faster clustering + richer compressed-label text processing
pip install "himalayas[speed,text]"Detailed installation options and fallback behavior are documented at himalayas-base.github.io/himalayas-docs/1_installation.
- Real-Valued Matrix Input: Operates on real-valued matrices encoding relationships among observations.
- Depth-Aware Cluster Definition: Cuts the dendrogram at a user-defined depth to define dendrogram-defined clusters for downstream analysis.
- Overrepresentation Testing: Uses a one-sided hypergeometric test to evaluate term enrichment in each cluster against the matrix background.
- Multiple-Testing Control: Supports Benjamini-Hochberg false discovery rate (FDR) correction for cluster-term tests.
- Annotation Mapping and Rendering: Maps significant annotations onto the clustered matrix and supports publication-ready matrix visualizations.
We applied HiMaLAYAS to a hierarchically clustered Saccharomyces cerevisiae genetic interaction profile similarity matrix (Costanzo et al., 2016), focusing on genes with high profile variance. Dendrogram-defined clusters were tested for Gene Ontology Biological Process (GO BP; Ashburner et al., 2000) enrichment, revealing hierarchical organization of biological processes.
HiMaLAYAS workflow and application to a hierarchically clustered yeast
genetic interaction profile similarity matrix (Costanzo et al., 2016).
A real-valued matrix and categorical annotations serve as inputs. The matrix is
cut at a user-defined depth, and each dendrogram-defined cluster is evaluated
for GO BP enrichment.
Horecka, I., and Röst, H. (2026)
HiMaLAYAS: enrichment-based annotation of hierarchically clustered matrices
bioRxiv. https://www.biorxiv.org/content/10.64898/2026.02.11.705303v2
Submitted to Bioinformatics Advances.
HiMaLAYAS software for the bioRxiv preprint.
Zenodo. https://doi.org/10.5281/zenodo.19338505
We welcome contributions from the community:
If you encounter issues or have suggestions for new features, please use the Issues Tracker on GitHub.
This project is distributed under the BSD 3-Clause License.