https://github.com/vitessce/paper-figures

https://github.com/vitessce/paper-figures

Last synced: about 4 hours ago
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• Host: GitHub
• URL: https://github.com/vitessce/paper-figures
• Owner: vitessce
• Created: 2023-01-20T22:20:37.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2023-11-15T21:07:24.000Z (12 months ago)
• Last Synced: 2023-11-15T22:26:47.245Z (12 months ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 2.98 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# vitessce-figures

## Setup

Create a conda environment

```sh

conda env create -f environment.yml

```

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

## Run

Activate the conda environment

```sh

conda activate vitessce-figures-env

```

```sh

# 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

```