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.
Currently this data is under embargo at GEO at GSE179640 to be released upon publication.
Additionally upon publication, the analyzed objects (in .h5ad
format) will be
available for download or exploratory viewing at the
JAX Single Cell portal.
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.
cd /path/for/manuscript/code
git clone https://github.com/TheJacksonLaboratory/endometriosis-scrnaseq.git
cd endometriosis-scrnaseq/data
ln -s /path/to/global_20201234.h5ad global.h5ad
ln -s /path/to/fibroblasts_20201234.h5ad fibro.h5ad
...
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 *