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.
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#
Contents