User: poisonAlien

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poisonAlien2.4k
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Cancer genomics

Posts by poisonAlien

<prev • 297 results • page 1 of 30 • next >
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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 4 days ago by poisonAlien2.4k
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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 24 days ago by poisonAlien2.4k
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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 weeks ago by poisonAlien2.4k
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Answer: A: Tools to identify the non-coding RNAs
... Try [lncRNA-screen][1] [1]: https://github.com/NYU-BFX/lncRNA-screen ...
written 8 weeks ago by poisonAlien2.4k
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Job: Bioinformatician - Cancer Genomics, Cancer Science Institute of Singapore, NUS, Singapore.
... We are seeking a bright, energetic individual with superior bioinformatic skills who can interact with approximately 10-15 post-docs/Ph.D. students; each of them are doing massively parallel sequencing of various tumors, RNA-Seq, ChIP-Seq, RNA array as well as combing the bioinformatics literature f ...
wxs R chip-seq job rna-seq written 8 weeks ago by poisonAlien2.4k
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Comment: C: Why copy number variations of TCGA is so high
... I believe that the papers that you're mentioning are looking at population based cnv's rather than sample wise. TCGA uses gistic to identify recurrent CN aberration in a cohort, which are potentially driver events. Above file is a CBS output and not all entries are copy number alterations. Last co ...
written 11 weeks ago by poisonAlien2.4k
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Comment: C: Why copy number variations of TCGA is so high
... how did you look at TCGA cnv data? Was it from GISTIC output ? ...
written 11 weeks ago by poisonAlien2.4k
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Comment: C: ABSOLUTE MAF error
... oh ! Okay, I think Absolute uses pre-computed purity and ploidy models from known cancer cohorts. I guess this is an issue if you're using non-human genome. ...
written 11 weeks ago by poisonAlien2.4k
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Comment: C: Germline mutation list in Lung TCGA data
... TCGA doesn't provide germline variants for privacy reasons. I think you will have to download BAM files and look by yourself. ...
written 12 weeks ago by poisonAlien2.4k
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Comment: C: ABSOLUTE MAF error
... Absolute requires column containing vaf, `t_vaf`. Maybe try adding it ? maf$t_vaf = as.numeric(as.character(maf$t_alt_count)) / as.numeric(as.character(maf$t_depth)) edit: also make sure chromosome names in MAF matches to that in segmentatioin file. Better remove `chr` prefix from both files. ...
written 12 weeks ago by poisonAlien2.4k

Latest awards to poisonAlien

Scholar 24 days ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 5 weeks ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Popular Question 8 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Appreciated 8 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 8 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 8 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Appreciated 9 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Appreciated 13 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 16 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 16 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Scholar 16 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?

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