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From @JPReceveur
Just went through and the extra prompts look good.
Random observation: when choosing 500 top genes, the number at the top shows 499 (dataset = 5dpf zebrafish, Piotrowski)
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Hello!
I have used cell2location to estimate cell abundances in several Visium libraries. Due to GPU constraints, I had to run each sample separately. I then re-load my anndata and model objects to…
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Hello! I am trying to generate the count matrix for the islet cell snATAC data by running **snATAC_pipeline.py** with fastq files pulled from GEO.
Unfortunately I am unable to run the whole pipelin…
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Dear scTE team,
I'm encountering a problem regarding the CR field in input bam files. In my bam files, corrected barcodes are stored in CB, while the uncorrected barcodes are in CR. A line of bam f…
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Hi,
I am having an issue exporting my h5ad file to spring for visualization. I have been following the [spring export tutorial](https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_ex…
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I am trying to call anndata with reticulate package (which is scRNA data). I can read anndata in %%R, I can access uns, and obs, but I can't access to anndata's raw data. (which is ndarray 2D data wit…
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Hi,
I used cell2location to find the cell type annotation in the MERFISH data using correspoding scRNA-seq data. I used the N_cells_per_location=1, and detection_alpha=20 parameter for the traini…
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It would be nice if we could seamlessly hold `dask` arrays and dataframes inside of an AnnData object.
I would consider this issue closed once most operations on an AnnData would work when it conta…
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Hi,
I perform batch correction using scVI. But I perform celltypist prediction before batch correction. Is it better to perform celltypist after batch correction or it doesn't matter?
Good day.