User: Tonny

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Tonny20
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New User
Location:
Shanghai, China
Last seen:
20 hours ago
Joined:
4 years, 4 months ago
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Posts by Tonny

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to import the output of CNVkit into GISTIC2.0 ?
... Hi Eric, I have tried the command as you mentioned. However, I failed to obtain the right markerFile. And I also tried to modify the start of segment with start_pos + 1. There were still segments with start or end positions do not match any markers in the markerFile. Finally, I found that 'As of GIS ...
written 1 day ago by Tonny20
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Comment: C: How to import the output of CNVkit into GISTIC2.0 ?
... Thanks for your answer. I will try it. ...
written 5 days ago by Tonny20
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How to import the output of CNVkit into GISTIC2.0 ?
... Hi, I get the many CNV results from sing cell genome sequencing with CNVkit. I'd like to get the driver CNV with GISTIC2.0. I have read the post https://www.biostars.org/p/158408/. There are two files, markerFile and segmentFile. Is there any way to obtain the files from the output of CNVkit? Than ...
cnvkit gistic2.0 written 12 days ago by Tonny20 • updated 10 days ago by Eric T.1.8k
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How to get the range of LOH?
... Hi, I need some help for the LOH in the output of CNVkit. How could I get the region of LOH for SciClone analysis? In the documentation I only find how to plot the LOH, and I'd like to get the detail information of these region. ...
cnvkit written 5 weeks ago by Tonny20 • updated 5 weeks ago by Eric T.1.8k
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How do I draw a heatmap in r with two colors in a cell?
... Hi, I've found some genes with different types of mutation in our sequencing project. I would like to draw a figure similar to it below. Is there any packages or software could do the job? I found ComplexHeatmap could show many information but without something I need. ![Example for heatmap][1] ...
R bioconductor complexheatmap written 9 weeks ago by Tonny20 • updated 9 weeks ago by EagleEye4.7k
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Comment: C: CNV detection of single cell genome sequencing
... Thank you for your reply. ...
written 10 weeks ago by Tonny20
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Comment: C: CNV detection of single cell genome sequencing
... Thank you for your reply. ...
written 10 weeks ago by Tonny20
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CNV detection of single cell genome sequencing
... Hi, I have some single cell genome sequencing data and I'd like to know if there is any good solution for CNV detection. I hear that CNVkit is a good choice to detect CNV for bulk data, but I don't google any thing about single cell. ...
cnvkit single cell genome sequencing cnv written 10 weeks ago by Tonny20 • updated 10 weeks ago by Eric T.1.8k
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How to add column name in facet_plot of ggtree
... I'd like to plot a multiple gheatmap with a phylogenetic tree using ggtree and facet_plot. my data is like this: >head(resis) A B C 1 SAMN00138235 MphC 0 2 SAMN00138235 MecR1 0 3 SAMN00138235 Aac6Ie 0 4 SAMN00138235 AadD 0 5 SAMN00138235 aad9Ib ...
R ggplot2 ggtree heatmap written 5 months ago by Tonny20 • updated 5 months ago by genomax33k

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