furry-couscous

Tools for manipulation and analysis of single-cell and spatial transcriptomic data

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Contents

scanpy_utils.py:

Contains functions for processing single-cell data in Python using Scanpy.

seurat_utils.r & ggplot_config.r:

Contains functions for processing single-cell data in R using Seurat.

fcc_utils.py:

Contains utility functions for manipulating datasets and comparing feature-reduced latent spaces.
Consult fcc_tutorial.ipynb for info on how to process datasets using the furry-couscous framework.

fcc.py:

Defines python classes for manipulation, processing, and visualization of scRNA-seq gene expression counts, dimensionality reduction objects, and spatial transcriptomics data.

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Required Python Dependencies

Several graph-based analysis packages require the iGraph C library. Ensure this is installed before proceeding.

Install Python packages using pip:

pip install -r requirements.txt