User: poisonAlien

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poisonAlien2.8k
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Cancer genomics

Posts by poisonAlien

<prev • 306 results • page 1 of 31 • next >
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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 12 months ago by poisonAlien2.8k
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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 12 months ago by poisonAlien2.8k
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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 19 months ago by poisonAlien2.8k
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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 19 months ago by poisonAlien2.8k
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Comment: C: detecting mutations in cancer samples belonging to the same cancer type
... Its using Mutect2 under the hood for variant calling and doing LOT of filtering to remove possible FPs and gremline variants - which is GOOD. I think you should try it! ...
written 20 months ago by poisonAlien2.8k
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Comment: C: detecting mutations in cancer samples belonging to the same cancer type
... If you have only tumor samples, no matter how much of a sophisticated algorithm you use - there is always an uncertainty associated with the somatic status of an identified variant. Having said that, MuTect can still call somatic variants without gremline controls. But again you will have to be care ...
written 20 months ago by poisonAlien2.8k
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Answer: A: Software to analyse mutational signatures other than DeconstructSigs R package
... There are few other tools. DeconstructSigs estimates loading of known signatures for every sample in the cohort. If you are interested in de-novo you could try [EMu](http://www.sanger.ac.uk/science/tools/emu) and [Mutational Signature framework](https://www.mathworks.com/matlabcentral/fileexchange/3 ...
written 21 months ago by poisonAlien2.8k
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Comment: C: Script for analyzing idat (illumina) microarray files with limma, any suggestion
... Try [Here](https://github.com/PoisonAlien/beadAnalyze) ...
written 21 months ago by poisonAlien2.8k
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Comment: C: Driver gene detection with SomInaClust
... Hi, You're passing MAF object as an input for `SomInaClust_det` function. My guess is it requires MAF file as an input. May be try this and see... ```r brca_Sominaclust <- SomInaClust_det(maf_brca, calculate_CDS = TRUE, convert_genenames_to_HGNC=FALSE) ``` ...
written 22 months ago by poisonAlien2.8k
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Answer: A: how to decide whether a mutation is driver for a specific cell line
... Hi, Whether a gene is a driver or not is usually done on large cohorts based on how frequently the gene is mutated. There are algorithms to identify such genes. How many cell lines do you have in your file ? In case if you're only interested in a particular mutation, - you will have to look at ...
written 24 months ago by poisonAlien2.8k

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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Appreciated 10 months ago, created a post with more than 5 votes. For A: Next Generation Sequencing
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Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
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Scholar 12 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
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Scholar 21 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
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Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
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Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
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Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP

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