User: el24

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el2410
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USA
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4 days, 9 hours ago
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6 months, 2 weeks ago
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Posts by el24

<prev • 17 results • page 1 of 2 • next >
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single cell ATAC-seq cicero gene activities in Seurat
... Hi everyone! I am loading my single-cell ATACseq data using cicero, and then I create gene activity scores according to the [tutorial][1]. My goal is to use this cicero gene activity score object in Seurat. Based on [Seurat][2], I can use cicero object in their pipeline as they mentioned that "Seur ...
single-cell scatacseq cicero seurat R written 14 days ago by el2410
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Comment: C: Result of scanpy tools rank_genes_groups
... Sorry for the confusion, I updated my response above as I forgot to write the to_df() function above but I had it in my code. I have used **n_genes=adata.to_df().shape[1]** so that part is fine and I could see the size of the output is as I expect. Although the other way also works for me - without ...
written 3 months ago by el2410
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Comment: C: Result of scanpy tools rank_genes_groups
... Yes, it's correct that the default is n_genes=100, but I'm using all available genes as n_genes=adata.to_df().shape[1] in my code. ...
written 3 months ago by el2410
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Comment: C: Result of scanpy tools rank_genes_groups
... Hi @shoujun.gu The reason is that they are all positive values so I was wondering how could it be possible?! unless these are absolute values for z score, but I am not sure. ...
written 3 months ago by el2410
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Result of scanpy tools rank_genes_groups
... Hi everyone, I'm clustering my single-cell data using Scanpy package, and I use [rank_gene_groups][1] to rank genes for characterizing groups. This returns names, scores, logfoldchanges, and pvals_adj for my Anndata format. I'm trying to interpret **scores** for this data, but I couldn't find any in ...
gene rank_gene_groups seurat clustering scanpy written 3 months ago by el2410
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Comment: C: Cellranger Reanalyze NO barcode rank plot in web_summary.html
... Sound good! Thanks for the information! ...
written 4 months ago by el2410
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Comment: C: Cellranger Reanalyze NO barcode rank plot in web_summary.html
... Thanks for checking, do you have any idea how can I safely remove the cells with fewer read values (which are not reliable) so that I can get the barcode rank plot and summary information in my web_summary.html? Also, do you usually recommend using any other parameters in "cellranger reanalyze" or y ...
written 4 months ago by el2410
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Cellranger Reanalyze NO barcode rank plot in web_summary.html
... Hi everyone, I have a question regarding running cellranger count on the data, I get the following warning after running it: Low Fraction Reads in Cells 68.5% Ideal > 70%. Application performance may be affected. Many of the reads were not assigned to cell-associated barcodes. T ...
warning reanalyze scrna cellranger written 4 months ago by el2410 • updated 4 months ago by swbarnes28.2k
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Comment: C: Extract data from a large bed file
... Thank you very much, this is very helpful! ...
written 4 months ago by el2410
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Extract data from a large bed file
... Hi all! I have a big .bed file, which is about 100GB of data, and I want to extract specific columns from it in a timely manner. I was wondering if there is a useful tool that works best for huge bed files. (or could be bed.gz) Could you please tell me if you know any excellent tool (or Python pack ...
genome bed alignment written 4 months ago by el2410 • updated 4 months ago by wm480

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