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LCA_csv2seurat.R (0.92 kB)
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LCA_h5ad2csv.py (1.31 kB)
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R/Python conversion

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posted on 2021-12-14, 18:50 authored by Angela PiscoAngela Pisco, The Tabula Microcebus Consortium
Instructions to read h5ad file in R: We provide Python and R scripts to convert a Python h5ad file into an R Seurat file. Please download the h5ad file of interest and Python script “LCA_h5ad2csv.py” to the same folder, and run in Python << python LCA_h5ad2csv.py -i input.h5ad -o output_folder -c layer_id >>, where input.h5ad is the h5ad file of interest, output_folder is the folder where the csv files will be exported, and layer_id is the gene count matrix to export (if layer_id = raw_counts, then the raw data is exported (adata.layers[‘raw_counts’]); if layer_id = log, then the log transformed data is exported (adata.X)). Then run “LCA_csv2seurat.R” in R to create a Seurat object from the csv files.

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