User: poisonAlien

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poisonAlien3.0k
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Cancer genomics

Posts by poisonAlien

<prev • 312 results • page 1 of 32 • next >
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Comment: C: trackplot: Fast and minimal dependency standalone R script to generate IGV style
... You are almost there. You just need to copy/move the binary to a `PATH` (e.g; `/usr/local/bin`) or to a directory under `PATH`. ...
written 6 weeks ago by poisonAlien3.0k
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Comment: C: trackplot: Fast and minimal dependency standalone R script to generate IGV style
... Thanks, @genomax and @ATpoint I have updated the repository. ...
written 7 weeks ago by poisonAlien3.0k
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Comment: C: trackplot: Fast and minimal dependency standalone R script to generate IGV style
... Thanks for testing and I am glad that you were able to make it work. I will make available the binaries soon :) edit: centOS and macOS binaries for bwtool are included in the repository. Thanks for the suggestion. ...
written 7 weeks ago by poisonAlien3.0k
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Comment: C: trackplot: Fast and minimal dependency standalone R script to generate IGV style
... I have tested quite throroughly on Ubuntu and CentOS. It works with no issues. Also, I do have a compiled version of bwtool on my mac (10.15.2), and I could not reproduce your errors. I guess opening an issue on `libbeato` might help to speed up debugging. edit: I am happy to share the bwtool mac b ...
written 7 weeks ago by poisonAlien3.0k
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Comment: C: trackplot: Fast and minimal dependency standalone R script to generate IGV style
... Try these [instructions](https://github.com/CRG-Barcelona/bwtool/issues/49#issuecomment-604477559) for bwtool compilation. It should work. Copied below as well. git clone 'https://github.com/CRG-Barcelona/bwtool' git clone 'https://github.com/CRG-Barcelona/libbeato' git clone https://g ...
written 7 weeks ago by poisonAlien3.0k
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Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
... If you are working with chip-seq or atac-seq or any assays resulting in bigWig files, one of the common visualizations is to generate track plots displaying signal intensities across genomic loci. Libraries in R like [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html) facilitates s ...
tool chip-seq bigwigs R visualization igv written 7 weeks ago by poisonAlien3.0k • updated 6 weeks ago by Sael20
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Comment: C: Recommendation for statistics book
... If I have to explain technicalities of PCA to a biologist, [this][1] is where I would start. [1]: https://www.youtube.com/watch?v=_UVHneBUBW0 ...
written 2.3 years ago by poisonAlien3.0k
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Answer: A: clonal populations in cancer samples
... To answer your question in a simple sentence - In an ideal scenario, variants with VAF around 50% is fully clonal. Since most somatic mutations tend to be heterozygous, a clonal mutation would have an allele frequency of 50%. Anything below ~45/40% would be a sub-clonal. But it also depends on your ...
written 2.3 years ago by poisonAlien3.0k
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Comment: C: TMB Tumor Mutation Burden
... I believe standard WXS capture sizes are around 50 mb. (eg; Agilent sure select) ...
written 2.9 years ago by poisonAlien3.0k
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Comment: C: How representative the solid tumor sample is to that entire tumor lesion in term
... I am not sure if I understand teh question correctly. But, you should look at one of those multi region WXS/WGS studies. Somatic mutation profile varies a lot within the bulk tumor based on biopsy site. So its pretty heterogeneous. ...
written 2.9 years ago by poisonAlien3.0k

Latest awards to poisonAlien

Popular Question 6 weeks ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Next Generation Sequencing
Appreciated 14 months ago, created a post with more than 5 votes. For A: Next Generation Sequencing
Popular Question 19 months ago, created a question with more than 1,000 views. For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Next Generation Sequencing
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Next Generation Sequencing
Scholar 2.3 years ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Scholar 3.1 years ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How to use Samtools to remove reads whose mate does not map as expected
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 3.3 years ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing

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