scAnalyzer Studio

Single-Cell RNA-seq & Spatial Transcriptomics Pipeline

1. Dataset & Organism

Organism

pbmc3k pbmc5k heart atlas mouse brain lung tumor Custom Upload

Quality Control

Min Genes & Max Genes

Max Mito % & Min Cells

Run Scrublet

Norm & Integration

Normalization

Imputation

k (Neighbors)

Threshold

n_pcs

Batch Correction

DimRed & Networks

PCA Comps

Neighbors (K)

UMAP

t-SNE

GRN Inference Transcription Factors (Comma Separated)

Analytics

Clustering & Res/K

Trajectory (Root & Branches)

Interactive HTML Plots:

2D UMAP 3D PCA t-SNE Violins Heatmap

1. Spatial Dataset & Organism

Organism

10x Visium Adult Mouse Brain (Default) Custom .h5ad Upload (Requires obsm['spatial'])

Quality Control

Min Counts per Spot Max Mito % Highly Variable Genes (n_top_genes)

DimRed & Clusters

PCA Comps & Neighbors (K)

Leiden Resolution

Spatial Analytics

Spatial Domains (K) Spatial Smoothing Weight (0.0 to 1.0) Top Spatial Variable Genes

Processing pipeline...

Keep an eye on your terminal. Large datasets will take time.

Success