CellPilot tutorials
Analysis Workflows
Choose a workflow below to open its tutorial. Please make sure you are using the lastest CellPilot version.
CellPilot is designed for biologists to analyze single-cell and spatial data without writing a single line of code. It directly accepts output files and folders from commercial platforms, including 10x Genomics Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC, Space Ranger, Xenium, Vizgen MERSCOPE MERFISH outputs, and NanoString CosMx outputs from AtoMx Spatial Informatics Platform.
For demonstration, these tutorials use public example datasets downloaded from 10x Genomics. Any command-line download or file-renaming steps are only for preparing those downloaded demo files. If you are using your own direct output from Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC, Space Ranger, Xenium, MERSCOPE, or CosMx/AtoMx, you normally do not need to rename files.
Single Cell Workflow
Single Cell Analysis
Spatial workflows
Spatial Analysis
Spatial Analysis - Xenium
Load Xenium output, inspect spatial coordinates, and explore transcript-level data.
05Spatial Analysis - VisiumHD
Run Visium HD sketching, clustering, region analysis, and spatial gene plots.
06Spatial Analysis - MERFISH
Analyze MERFISH spatial expression data and cell-level annotations.
07Spatial Analysis - CosMx
Import CosMx datasets and review spatial clusters, regions, and gene patterns.
Multiple sample analysis
Integration
scRNA-seq Integration
Combine multiple scRNA-seq samples and compare shared cell populations.
09scATAC-seq Integration
Integrate chromatin accessibility datasets across samples or conditions.
10scMultiome Integration
Align paired multiome samples while preserving RNA and ATAC context.
11Spatial Integration
Integrate spatial datasets such as Xenium and Visium HD across slides, samples, or conditions.
Guided analysis
Agent Mode
Connect to AI assistants