Manuscript
CoSTA: Unsupervised Convolutional Neural Network Learning for Spatial Transcriptomics Analysis
CoSTA is an analysis approach for understanding spatial gene relationship of spatial transcriptomics.
To reproduce results in Manuscript, please follow instruction in notebook tutorial under the foder of "CoSTA".
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|----Analyzing_Slide-seq_via_CoSTA.ipynb
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|----Analyzing_MERFISH_via_CoSTA.ipynb
Analysis about comparison with SPARK and SpatialDE is in the folder of "analysis"
- NumPy
- SciPy
- Pandas
- Scikit-learn
- NaiveDE
- Pytorch
For processed data provided in the data folder, images are flattened by row, so that each row contains the full image for a given gene, indicated in the first column. The last two columns "x" and "y" specify the the dimension of the image.