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Hi Aaron,
I used `read10xCounts(..., type = "HDF5")` to load a HDF5 file from CellRanger v3.
I was surprised to get an error when I then ran `scater::calculateQCMetrics()` on the result.
Ultimately…
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Hi,
I have a simple question. I am looking at the .clones.tsv output for the single-cell Mixcr workflow, and there are often multiple clones per cell barcode. Should I just use the first one with …
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Hi Alex,
Thanks for developing such an amazing tool.
I run STARsolo on the single cell RNAseq data.
Since I want to have more insights into two similar genes, I added `--soloMultiMappers Uniform…
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Hi,
I'm using STARsolo v2.7.10b to align reads generated by 3prime or 5prime 10X libraries, and I want to output the BAM file aligned to transcriptome, so I'm using the `--quantMode TranscriptomeSA…
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I am new to Single-Cell Sequencing Analysis and coding, but I am working on analyzing some sequencing data and comparing interactions between cells.
I followed the CellPhone DB tutorials to prepare…
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Hey there
I'm using tiledb.from_pandas to create a tiledb array from a pandas dataframe.
My question regards the *sparse* parameter of the *from_pandas* function.
My dataframe mostly consists o…
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Hi and thanks for developing this very useful tool!
when i tried to use snapatac2.tl.add_cor_scores(network, peak_mat= data) it gives me error of "'NoneType' object has no attribute 'obs_names'"
da…
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Hi,
I encountered these two errors while running velocyto... the loom file is created.
2019-02-03 22:25:37,857 - DEBUG - Counting done!
2019-02-03 22:25:38,494 - DEBUG - Example of barcode: AGG…
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hi，i got an erro below,when i run function run_de
r$> DE = run_de(sce)
Error in `$
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If you dig in their github repository you will likely find the data already summarised for you in form of R script for reproducibility, so you have to avoid the 95% of work in getting raw single-cell …