readme

README.md

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+# Single Cell Analysis Applications in Python
+
+This repository contains applications of [Scanpy](https://github.com/theislab/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](https://github.com/theislab/scanpy). 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](https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html) and [here](https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html)
+
+## 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
+```
+
+
+<!-- ### Prerequisites
+
+What things you need to install the software and how to install them
+
+```
+Give examples
+```
+
+### Installing
+
+A step by step series of examples that tell you how to get a development env running
+
+Say what the step will be
+
+```
+Give the example
+```
+
+And repeat
+
+```
+until finished
+```
+
+End with an example of getting some data out of the system or using it for a little demo
+
+## Running the tests
+
+Explain how to run the automated tests for this system
+
+### Break down into end to end tests
+
+Explain what these tests test and why
+
+```
+Give an example
+```
+
+### And coding style tests
+
+Explain what these tests test and why
+
+```
+Give an example
+``` -->
+
+## Authors
+
+* **Joshua Wu** [email protected]
+* **Mike Czerwinski** [email protected]
+
+Any questions, comments and/or feedback are welcome!
+
+## Acknowledgments
+
+* [**Jason Spence Lab**](http://www.jasonspencelab.com/) for support from our colleagues
+* [**Theis Lab**](https://github.com/theislab) and [**Satija Lab**](https://satijalab.org/) for their work on modern single cell analysis techniques