10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger1.3, printed on 11/05/2024

Secondary Analysis in Python

The primary outputs of Cell Ranger (gene-barcode matrix, PCA, t-SNE, and clustering) can easily be loaded into Python for further analysis.

We recommend installing Anaconda, which includes the interactive Jupyter Notebook as well as a full suite of packages that can be used for analysis and visualization.

Python Analysis Example

Here is some example code for loading the 1.3 Million Brain Cells from E18 Mice dataset:

• 1.3M Cell Tutorial (Jupyter Notebook)
• 1.3M Cell Tutorial (HTML)

This notebook demonstrates:

• loading / saving a gene-barcode matrix in HDF5 format
• loading / saving analysis files in CSV format
• subsampling barcodes
• plotting UMI and gene count distributions
• plotting clustering results and gene-specific expression in TSNE space

Although this example uses the 1.3M cell dataset, the code can be used to load any Cell Ranger dataset.