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10x Genomics
Chromium Single Cell Gene Expression

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.

If you are a developer of scRNA-seq analysis software and would like to be listed here, please e-mail opensource@10xgenomics.com.

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:

This notebook demonstrates:

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