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.
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
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
- Joshua Wu wujos@med.umich.edu
- Mike Czerwinski czerwmj@med.umich.edu
Any questions, comments and/or feedback are welcome!
- Jason Spence Lab for support from our colleagues
- Theis Lab and Satija Lab for their work on modern single cell analysis techniques