SCALA+

Thu, 12 Nov 2026 00:00:00 +0000

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 , 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 . 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.

SCALA+ is licensed under the GNU General Public License v3.0.

ScRNA | Manabe Lab

SCALA+

SCALA+

New Modules

Rewritten Modules

Getting Started

Citation