10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger2.1, printed on 11/05/2024

Secondary Analysis in Python

Third-Party Analysis Packages

The bioinformatics community is actively developing software to analyze Chromium Single Cell data. See below for some featured examples. These packages are not supported by 10x Genomics.

• scanpy by the Theis Lab.
  • scanpy GitHub page

If you are a developer of scRNA-seq analysis software and would like to be listed here, please e-mail [email protected].

Python Analysis Example

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.

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.