A repo for hosting the shiny application code for human blastoids fidelity assessment based on the study of Systematic transcriptomic evaluation of blastoid models of early human development
The application allows users to explore the human blastoid benchmarking results and evaluate a query dataset against the integrated human embryo reference.
The hosted application is available at:
https://shiny.maths.usyd.edu.au/blastoid_shiny/
blastoidShiny/
├── app.R
├── helper.R
├── data/
└── www/
app.R: user interface and server componentshelper.R: data processing, evaluation and plotting functionsdata/: data objects required by the applicationwww/: images and other static application resources
The processed human embryo atlas, blastoid benchmarking results and data objects required by the application are available from Zenodo:
https://doi.org/10.5281/zenodo.21824292
Download the Zenodo archive and copy the contents of its shiny_app_data/ directory into the data/ directory of this repository without changing the filenames.
Install the required R packages, open R in the repository directory and run:
shiny::runApp(".")Alternatively, specify the full repository path:
shiny::runApp("/path/to/blastoidShiny")The application was developed in R and uses Shiny, Seurat/SingleCellExperiment and associated analysis and visualization packages.
The study analyzes previously published human embryo, blastoid and non-human-primate embryo datasets. Accession numbers and source publications are provided in the manuscript's Key Resources Table.
Original sequencing data are not redistributed in this repository.
If you use this application or the associated resources, please cite:
Long S, Kim HJ, Salehin N, Huang H, Zhang X, Jothi R, and Yang P. Systematic transcriptomic evaluation of blastoid models of early human development. Publication details to be updated.
Please also cite the associated Zenodo record:
https://doi.org/10.5281/zenodo.21824292
For questions or additional information, contact:
Siqu Long
slong@cmri.org.au