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Update README.md
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ttgump authored May 10, 2023
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Expand Up @@ -10,6 +10,7 @@ SpaVAE, spaPeakVAE, spaMultiVAE, and spaLDVAE are dependency-aware deep generati
- [Network diagram](#diagram)
- [Requirements](#requirements)
- [Usage](#usage)
- [API documents](#api)
- [Parameters](#parameters)
- [Datasets](#datasets)
- [Reference](#reference)
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--data_file specifies the data file name, in the h5 file. For SRT data, spot-by-gene count matrix is stored in "X" and 2D location is stored in "pos". For spatial ATAC-seq data, "X" represents spot-by-peak count matrix. For spatial multi-omics data, "X_gene" represents spot-by-gene count matrix, and "X_protein" represents spot-by-protein count matrix.

## <a name="api"></a>API documents

https://github.com/ttgump/spaVAE/wiki

## <a name="parameters"></a>Parameters
**--data_file:** data file name.<br/>
**--select_genes:** number of selected genes for embedding analysis, default = 0 means no filtering. It will use the mean-variance relationship to select informative genes.<br/>
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