Single-Cell RNA-seq Exploration App
This application provides interactive exploration of single-cell / single-nuclei RNA-seq datasets of mouse skeletal muscle. It accompanies the study of muscle homeostasis and regeneration in wild-type (WT) and dystrophic (MDX) mice across genetic backgrounds (C57BL/6J, DBA/2J) and ages, covering the major mononuclear cell populations of the muscle microenvironment.
Four datasets can be explored: the full integrated atlas (all cell types), and three focused subclusterings of the fibro/adipogenic progenitors (FAP), the macrophage compartment, and the myogenic lineage (MuSCs, myoblasts, myocytes, myofibers).
Use the tabs above to visualize cluster structure and embeddings, inspect gene expression on the cell map, compare expression across groups with violin and dot plots, browse per-cluster marker genes, and analyze cell type composition across samples and conditions.
Methods summary
Processing performed with Seurat: QC filtering (nFeature/nCount, mitochondrial percentage), doublet detection with scDblFinder, SCTransform normalization, dimensionality reduction (PCA / UMAP), batch integration with Harmony, graph-based clustering and marker detection with FindAllMarkers().
Citation
If you use this app or the underlying data, please cite the Zenodo archive:
