Welcome to EnrichMap's documentation! ===================================== **EnrichMap** performs gene set enrichment analysis on spatial transcriptomics data, with gene weight inference and geostatistical modelling of spatial structure. It enables pathway-level mapping and comparison of opposing programmes across platforms, with outputs designed for direct interpretation. .. image:: https://github.com/secrierlab/enrichmap/raw/main/img/enrichmap_workflow.jpg :alt: EnrichMap workflow :align: center Features -------- - Efficient computation of gene set enrichment scores in spatial data - Gene weight inference within pathways and across opposing programmes - Spatial smoothing and correction for spatial covariates - Optional batch correction (recommended mode) for multi-sample integration - Geostatistical diagnostics to quantify spatial structure - Compatibility with major platforms (e.g. Visium, Visium HD, Xenium, MERFISH, etc.) - Native support for AnnData (.h5ad) objects - Direct visualisation of spatial enrichment maps Documentation ------------- Comprehensive documentation is available at: https://enrichmap.readthedocs.io/en/latest Contributing ------------ If you have ideas for new features or spot a bug, please open an issue or submit a pull request. License ------- This project is licensed under the GNU GENERAL PUBLIC LICENSE. Citation -------- Celik C & Secrier M (2025). *EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics*. `biorxiv.com `_ Copyright --------- This program is free software: you can redistribute it and/or modify it under the terms of the `GNU General Public License `_ as published by the Free Software Foundation, either version 3 of the License or any later version. This program is distributed in the hope that it will be useful, but **WITHOUT ANY WARRANTY**, without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Contents -------- .. toctree:: :maxdepth: 2 :caption: Contents install usage tutorials/index api