Cytocipher Manuscript code

Reproduces analyses for the Cytocipher manuscript.

Installation and Getting started

Installation:

conda create -n cytocipher_ms python=3.8.12
conda activate cytocipher_ms
pip install -r requirements.txt
git clone https://github.com/BradBalderson/Cytocipher_manuscript.git

Start:

cd Cytocipher_manuscript
jupyter notebook

Quick index

Quick explanation of respository structure.

For information on individual jupyter notebooks, see docs/index.md.

scripts/

X1_pbmc3k/
    -> Code for automatic download and analysis of 10X PBMC 3K data.

X2_simulation/
    -> Code for simulated data generation and analysis.
    
X3_e18_hypo_neurons/
    -> Code for analysis of hypothalamus E18.5 neurons, from paper:
       B. Yaghemaian, B. Balderson, et al. (2022) doi.org/10.1242/dev.200076

X4_pancreas/
    -> Code for automatic download and analysis of pancreatic dev. data.
    
X5_prostate/
    -> Code for automatic download and analysis of prostate cancer data.
    
X6_tabula_sapiens/
    -> Code with download instructions and analysis of Tabula Sapiens data.