SYSMIOME is an integrated toolbox for microbiome data analysis designed for clinical research. It provides a comprehensive workflow for processing, exploring, and visualizing microbiome datasets while ensuring data security through a Docker-based local implementation.
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System Requirements:
- Linux environment
- R
- Docker (for local deployment)
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Data Requirements:
- OTU abundance tables
- Corresponding sample metadata
You can view a live demo here
- Alpha Diversity visualization
- Beta Diversity visualization
- Taxonomy visualization
- Correlation analyis
SYSMIOME offers a Docker image for local deployment, ensuring that analyses are conducted within a secure and controlled environment—a critical feature for clinical projects handling sensitive data. Note: The data downloaded via the wget command includes the supplementary datasets used to illustrate the toolbox in two prospective clinical studies.
# Download and extract the data first (if not already done)
wget --content-disposition https://osf.io/gfhx2/download && tar -xzf sysmiome_data.tar.gz && rm sysmiome_data.tar.gz
# Copy files from local extracted folder into the volume
docker run --rm \
-v sysmiome_data:/data \
-v "$(pwd)/sysmiome_data":/from_host \
alpine:3.21.3 cp -r /from_host/. /data/ &&
rm -r ./sysmiome_data
docker run --rm \
-v sysmiome_data:/data \
alpine:3.21.3 sh -c "chmod -R a+rwX /data"
docker run --rm -p 6644:3838 \
--user shiny \
--group-add $(id -g) \
-v sysmiome_data:/sysmiome \
yumyai/sysmiome-serve:0.0.7-devThe local installation should be http://localhost:6644/.
This project is licensed under the Apache License 2.0.
For questions or support, please contact yumyai@gmail.com or open an issue on the GitHub repository.