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Hi!
Our scRNA-seq data was processed using the Seurat package. In order to run scDRS with our scRNA-seq data, I first converted the Seurat object saved as an RDS file to an h5ad file using the foll…
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I get an error when I use sc.read_10x_mtx() to read scRNA-seq files (matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz) generated by "Illumina HiSeq 4000". The function works fine when I read files …
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Hi,
I tried integrating three PBMC snRNAseq data from 10X Genomics multiome datasets with two scRNA seq data from a 10X Genomics Public dataset. However, all the data from the multiome clusters sep…
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Are raw counts available for the scRNA-seq data? From the commands history in the Seurat object, seems like the data in the "RNA" slot under assays is normalized.
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**User story**
Part of the epic https://github.com/sanger/limber/issues/1713. Check the 'work completion' code works properly, to automatically pass the cell extraction requests.
**Who are the p…
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Hi,
I am going to use SCATS to analyze 10x scRNA-seq data. After running cellranger, I can only get one bam file containing many cells. How can I generate metafile for SCATS step2? Can you give an ex…
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Hi Michael,
Sorry for all the questions. This might be a bit naive.
I was just wondering how you went about processing the matrices outputted from the pipeline to construct a counts matrix...? …
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I am working with scRNA-seq data that consists of various cell groups from a total of 9 samples. The dataset contains over 1 million cells. When I run StemFinder on the entire dataset, the calculation…
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- In my opinion the markers are too large, even for relatively few datapoints (even worse for more datapoints)
- For metadata plots one cannot nicely see how diverse clouds of data are since they are…