Endometriosis scRNA-seq

This repository accompanies the manuscript

Tan Y, Flynn WF, Sivajothi S, Bozal S, Luo D, Luciano AA, Robson P, Luciano DE, Courtois ETC. "Cellular Phenotyping of Endometriosis at the single cell level highlights complex heterogeneity" (2020) currently available on bioRxiv.

Data Availability

Raw and processed data

Currently this data is under embargo at GEO at GSE179640 to be released upon publication.

Analyzed data objects

Additionally upon publication, the analyzed objects (in .h5ad format) will be available for download or exploratory viewing at the JAX Single Cell portal.

Issues with this code or repository

We are committed to making this analysis and its accompanying figures reproducible. If you experience problems, a bug, a question, etc., please open an issue and tag @wflynny or @yulianatan.

For development

1. Clone this repository somewhere with

   cd /path/for/manuscript/code
   git clone https://github.com/TheJacksonLaboratory/endometriosis-scrnaseq.git
   

2. Link for data objects:

   cd endometriosis-scrnaseq/data
   ln -s /path/to/global_20201234.h5ad global.h5ad
   ln -s /path/to/fibroblasts_20201234.h5ad fibro.h5ad
   ...
   

3. Make a notebook in the notebooks folder.
4. In that notebook, do the following after your standard imports:

   import os, sys
   sys.path.append(f"{os.getcwd()}/../code")
   from plotting.plot_settings import *
   from plotting.palettes import *
   from plotting.scatter import *
   from plotting.matrix import *