User: amjad

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amjad80
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Posts by amjad

<prev • 14 results • page 1 of 2 • next >
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Comment: C: ctDNAtools: an R package to work with ctDNA sequencing data
... Hi Peter, you are right that the output should list these mutations (which could be a future feature). For now you can just run: filter_mutations(mutations, black_list = black_list1, substitution_specific = FALSE) It will output a dataframe with the left mutations after filtering. ...
written 13 hours ago by amjad80
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Comment: C: ctDNAtools: an R package to work with ctDNA sequencing data
... For more details check the manuscript in BioRxiv: https://www.biorxiv.org/content/10.1101/2020.01.27.912790v1 ...
written 22 days ago by amjad80
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Answer: A: ctDNAtools: an R package to work with ctDNA sequencing data
... For more details check the manuscript in BioRxiv: https://www.biorxiv.org/content/10.1101/2020.01.27.912790v1 ...
written 22 days ago by amjad80
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Tool: ctDNAtools: an R package to work with ctDNA sequencing data
... Dear community, I am pleased to share with you the R package I have developed for analysis of ctDNA sequencing data (ctDNAtools). https://github.com/alkodsi/ctDNAtools You can do two kinds of analyses with ctDNAtools: 1. Minimal residual disease testing: this is useful if you have a list of pre ...
tool ngs sequencing ctdna liquid-biopsy cancer-genomics written 4 weeks ago by amjad80
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Comment: C: Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing
... Unfortunately, ctDNAtools wouldn't be useful to compare relapse to primary. But you can check this article for some insight: https://www.nature.com/articles/s41591-019-0561-9.pdf?draft=collection Hope this helps. ...
written 4 weeks ago by amjad80
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Comment: C: Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing
... There will be a BiorXiv manuscript soon (in 2-3 days) describing what you can do with ctDNAtools. For now you can browse the vignette. Briefly, there are two main analyses you can do: (1) sequencing reads fragmentation: this is only relevant if you have ctDNA data because ctDNA would be fragmented b ...
written 5 weeks ago by amjad80
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Answer: A: ides capp-seq bioinformatics pipeline
... You can try an alternative approach implemented in the ctDNAtools R package: https://github.com/alkodsi/ctDNAtools In ctDNAtools, you can use a black list which serves in a way a similar task to the background polishing. The duplex barcode processing needs to be done on your alignment data. You ca ...
written 5 weeks ago by amjad80
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Answer: A: ctDNA fraction calculation
... If you are interested in testing whether there is any fraction of ctDNA in plasma or not rather than quantifying the amount, you may be interested in checking the ctDNAtools R package: https://github.com/alkodsi/ctDNAtools ...
written 5 weeks ago by amjad80
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Answer: A: Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing
... You can check the ctDNAtools R package if it suits your needs. From a cancer detection perspective, it doesn't matter if your data is from ctDNA or CTC. However, you would need a list of mutations to use for tracking the tumor. https://github.com/alkodsi/ctDNAtools ...
written 5 weeks ago by amjad80
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Comment: C: Can germline vs somatic variants be distinguished by phasing when no control is
... Thanks for the answer. Actually we are confident about the somatic origin of the blue one because we do have a related cancer sample that doesn't show that mutation. The confusion is about the other two and it's good to know that there is no way to confirm that. ...
written 4.2 years ago by amjad80

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