Single Cell Spatial Transcriptomics of the Murine Embryonic Palate Links Pax9 to Patterning and Organization of Extracellular Matrix Components

This repository hosts the codes for the original analysis of GSE284271.

Prerequisites

To reproduce the results of our published article, the output of spaceranger has to be prepared by using all data from GSE284271 by yourself.

We recommend opening the 00.NIH_10xVisiumHD.rmd R notebook file by using Rstudio.

We recommend opening the 01.scRNAseq10xVisiumHD.ipynb file by using the Python Jupyter Notebook.

The OS platform, R environments, R packages, and Python modules can be checked in the sessionInfo() results under the Supplementary section of the analysis report and the Jupyter Notebook results.

To check the original results as same as in our original article, please visit our analysis report website (https://labonom.github.io/GSE284271/01.scRNAseq10xVisiumHD.html).

Contact

WANG Ziyi
E-mail: wangziyi@s.okayama-u.ac.jp

Bioinformatics Study Group in Okayama University Software License

Bioinformatics Study Group in Okayama University Software License – This software license is the 2-clause BSD license plus clause a third clause that prohibits redistribution and use for commercial purposes without further permission.

Copyright © 2024. Bioinformatics Study Group in Okayama University. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Redistributions and use for commercial purposes are not permitted without the Bioinformatics Study Group in Okayama University’s written permission. For purposes of this license, commercial purposes are the incorporation of the Bioinformatics Study Group in Okayama University’s software into anything for which you will charge fees or other compensation or use of the software to perform a commercial service for a third party. Contact wangziyi@s.okayama-u.ac.jp for commercial licensing opportunities.

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