Reproducible comparative single-cell atlas for the evolution of decidualization across mammals.
Repository: github.com/BioNanomics/ConvergentDecidua
ConvergentDecidua builds a cross-species single-cell atlas to investigate how spontaneous decidualization evolved independently in menstruating mammals. The pipeline ingests public scRNA-seq, scATAC-seq, and bulk RNA-seq datasets from human and mouse, maps orthologs, integrates stromal cell populations, and scores decidualization-related gene modules.
wombat CLI — Command-line interface for all pipeline steps (Click-based)| Step | Result |
|---|---|
| Ortholog backbone | 25,439 human↔mouse pairs via Ensembl Compara |
| Datasets | GSE127918, GSE111976 (human scRNA), GSE226429 (mouse bulk) |
| Integration | Harmony on 9,065 human stromal cells, 4 subtypes identified |
| Scoring | 8 modules scored (decidual, progesterone response, senescence, etc.) |
If you use this software, please cite using the CITATION.cff file.