SCALA+
SCALA+
SCALA+ is an R/Shiny web application for multimodal analysis of single-cell next-generation sequencing data. It is a modified and extended version of SCALA, originally developed at the Biomedical Sciences Research Center “Alexander Fleming”, which we have been extending since 2023. SCALA+ is fully compatible with Seurat v5 and adds many analytical capabilities.
New Modules
- Data import: h5ad (AnnData), CellBender h5, and qs/qs2 files
- Spatial transcriptomics: Visium data import and analysis; BANKSY spatially-aware clustering
- Quality control: Sample demultiplexing (hashDemux, demuxmix, deMULTIplex2), DropletQC, CellBender remove-background, and scDblFinder doublet detection
- Batch correction and integration: Harmony, Scanorama, FastMNN, SCTransform, and Seurat v5
IntegrateLayers(CCA, RPCA, Joint PCA) - Clustering: Leiden clustering (replacing Louvain)
- Expression analysis: DEG analysis (separate from marker identification), pseudobulk analysis, and gene set scores (UCell, GSDensity)
- Cell–cell communication and trajectories: CellChat and Velocyto RNA velocity
Rewritten Modules
- SCENIC / pySCENIC: Gene regulatory network analysis
- NicheNet: Ligand–receptor analysis (v2 databases)
- Slingshot: Trajectory analysis
Getting Started
For installation instructions and basic usage, please refer to the original SCALA repository. The SCALA+ code is available on GitHub:
Citation
If you use SCALA+, please cite the original SCALA paper:
Tzaferis C, Karatzas E, Baltoumas FA, Pavlopoulos GA, Kollias G, Konstantopoulos D. SCALA: A web application for multimodal analysis of single cell next generation sequencing data. Comput Struct Biotechnol J 2023. doi:10.1016/j.csbj.2023.10.032
SCALA+ is licensed under the GNU General Public License v3.0.