README.md

vitessce-figures

Setup

Create a conda environment

conda env create -f environment.yml

Install Globus Connect Personal - see comments in ./codex/Snakefile for more details

Run

Activate the conda environment

conda activate vitessce-figures-env

# Vignette 01
cd osmfish
snakemake -j 1
cd ..
jupyter lab
# Run all cells of osmfish/src/osmfish.ipynb

# Vignette 02
cd visium
snakemake -j 1
cd ..
jupyter lab
# Run all cells of visium/src/visium.ipynb

# Vignette 03
cd ims
snakemake -j 1
cd ..
jupyter lab
# Run all cells of ims/src/ims.ipynb

# Vignette 04
cd codex
snakemake -j 1
cd ..
jupyter lab
# Run all cells of codex/src/codex.ipynb

# Vignette 05
cd cite-seq
snakemake -j 1
cd ..
jupyter lab
# Run all cells of cite-seq/src/cite-seq.ipynb

# Vignette 06
cd multiome
jupyter lab
# Run all cells of multiome/src/multiome.ipynb