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Graphene-seq

Code and source data used for graphene-based optically clear in situ sequencing and electrophysiology analyses.

Repository Layout

  • notebooks/: Figure and supplementary figure notebooks.
  • src/graphene_electro_seq_analysis/: Analysis utilities used by notebooks.
  • SourceData/: Preprocessed data and source data tables.

Requirements

  • Python 3.8
  • Jupyter Notebook
  • Common packages: numpy, pandas, scipy, matplotlib, seaborn, scanpy, anndata, scikit-learn

Install dependencies in your preferred environment and run notebooks in order.

Usage

  1. Create and activate a Python 3.8 environment.
  2. Launch Jupyter Notebook from the repository root.
  3. Open a notebook in notebooks/ and run cells top to bottom.

External Code

The file src/graphene_electro_seq_analysis/importrhdutilities.py is from: https://github.com/Intan-Technologies/load-rhd-notebook-python