Multi-sample integration
Batch correction with Harmony, Scanorama, ComBat or BBKNN for cohort-level analyses.
Open Integration
Upload data, run quality control, build embeddings, detect markers, annotate cell types, compare mRNA expression across saved analyses, and export results from one guided interface.
Each module keeps parameters visible and produces reusable artifacts, so runs can be resumed, compared and cited.
scExplorer keeps advanced methods close to the pipeline while preserving the outputs needed for interpretation and reproducibility.
Batch correction with Harmony, Scanorama, ComBat or BBKNN for cohort-level analyses.
Open IntegrationUMAP, gene-level plots, dot plots, violin plots and heatmaps with accessible themes.
Open VisualizationTrajectory inference, RNA velocity, SCENIC regulons and CellChat communication analysis.
Open DownstreamLong-running steps execute in the background with status tracking and reusable artifacts.
Import compatible public datasets from GEO, CELLxGENE, HCA and related portals.
Download ConnectorParameter guidance, method notes, diagrams and glossary entries for each workflow stage.
Open GuideLocal installation supports Linux, macOS and Windows through Docker, allowing private data handling and use of local computational resources. Installation details are available in the GitHub repository.
If you use scExplorer in your research, please cite:
Sergio Hernández-Galaz, Andrés Hernández-Oliveras, Felipe Villanelo, Alvaro Lladser, Alberto J M Martin, scExplorer: a comprehensive web server for single-cell RNA sequencing data analysis, Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf273, https://doi.org/10.1093/bioadv/vbaf273