Chromium Single Cell Gene Expression
Cell Ranger3.0, printed on 02/21/2024
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
- scanpy 1.3.3 or above is required to work with Cell Ranger 3.0 outputs.
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 (feature-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 10k Cells from E18 Mice dataset:
This notebook demonstrates:
- Loading a feature-barcode matrix in HDF5 format.
- Loading analysis files in CSV format.
- Plotting UMI and feature (gene) count distributions.
- Plotting clustering results and gene-specific expression in t-SNE space.