Interface Guide

Interface Guide

Dataset tab

• Upload Data — upload a .rds / .qs2 Seurat object, or click Download and Run a demo data.
• Data Overview — total cells, genes, clusters and assays.

Explorer menu

Available after data is loaded:

Page	What it does
Dim Reduction Plot	Visualize cells in UMAP / t-SNE / PCA, colored by cluster or split by metadata.
Feature Plot	Overlay gene expression on a dimensionality-reduction plot.
Violin Plot	Compare gene-expression distributions across clusters.
Dot Plot	Expression percentage and average level across clusters (dot matrix).
Heatmap Cell Level	Single-cell gene-expression heatmap.
Heatmap Group Averaged	Heatmap of per-cluster averaged expression.
Ridge Plot	Expression density ridges across clusters.
Cell Percentage Plot	Cell-type proportion across samples/groups.
DEGs Analysis	Cluster markers, or differential genes between two custom groups.
Top Expressed Features	Highly expressed genes per cluster (by cell or by accumulated UMI).
Feature Summary	Mean / median / percentage expression per cluster.
Feature Correlation	Gene-gene expression correlations.
Rename Clusters	Interactively rename cluster labels (session-only).
Gene Based Cluster (BETA)	Group cells by a gene's expression with custom cutoffs.
Combination Based Cluster (BETA)	Combine two cluster annotations into a new grouping.
Module Score (BETA)	Score cells with a gene set via AddModuleScore.
Search Features	Search/browse feature names across assays; ATAC annotations with Signac.
Cells Metadata	Browse and download cell-level metadata (CSV).
Object Structure	Inspect the structure of the Seurat object.
About	In-app information.

Once data is loaded, a Settings entry also appears (used by the SeuratExplorerServer deployment).

Notes on interactive annotation

Rename Clusters, Gene Based Cluster, Combination Based Cluster and Module Score add new metadata columns in the current session only — the original file is never modified. Downloadable mapping files let a bioinformatician apply changes permanently.