User: poisonAlien

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Cancer genomics

Posts by poisonAlien

<prev • 304 results • page 1 of 31 • next >
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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 8 weeks ago by poisonAlien2.5k
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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 8 weeks ago by poisonAlien2.5k
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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 12 weeks ago by poisonAlien2.5k
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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 3 months ago by poisonAlien2.5k
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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 3 months ago by poisonAlien2.5k
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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 3 months ago by poisonAlien2.5k
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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 4 months ago by poisonAlien2.5k
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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 6 months ago by poisonAlien2.5k
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Answer: A: Annotation of ID from TCGA gene expression data
... They are Ensemble Gene IDs. See [here][1] for converting them to Gene symbols. [1]: http://www.ensembl.org/Help/Faq?id=125 ...
written 6 months ago by poisonAlien2.5k
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Comment: C: Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
... > The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was > something unncessarily invented and confusingly named for cancer > genetics. So true! This also conflicts with [Multiple Alignment Format][1] [1]: https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5 ...
written 7 months ago by poisonAlien2.5k

Latest awards to poisonAlien

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 3 months ago, created a question with more than 1,000 views. For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Scholar 4 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Popular Question 4 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 6 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Teacher 6 months 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
Scholar 6 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 7 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Popular Question 14 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Appreciated 14 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 14 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 15 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Appreciated 15 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 15 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Scholar 15 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing

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