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Single Cell Analysis Applications in Python

This repository contains applications of Scanpy used by the Jason Spence Lab. basic_analysis_script.py contains a basic outline to run a single cell RNA sequencing analysis. scanpy_spence.py contains our collection of functions used to run the analysis.

Getting Started

To run this project, install Scanpy from here. Make sure to have a recent version of Python. As of June 2019, we are using Python version 3.7.3.

To understand the single cell analysis tools, check out the Scanpy and Seurat tutorials side-by-side here and here

Data Storage

We keep track of our data using a meta-data table in a .tsv file. Each sample is represented in the table with the following format

<Sample ID Number> <path/from/storage_mount_point/to/raw_data_matrix.h5> <metadata fields>

Example

2182-1 01_RNAseq_RAW_Data/Run_2182_Czerwinski_HIO_fetal_intestine_scRNAseq/Data/Intensities/BaseCalls/1-HIO-Fresh/outs/filtered_gene_bc_matrices_h5.h5 age:30 tissue:HIO gel:Matrigel media:ENR sex:Male sampleName:1-HIO-Fresh

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Any questions, comments and/or feedback are welcome!

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