User: poisonAlien

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poisonAlien2.4k
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Cancer genomics

Posts by poisonAlien

<prev • 294 results • page 1 of 30 • next >
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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 1 day 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 2 days 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 21 days 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 21 days 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 22 days 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 24 days 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 24 days ago by poisonAlien2.4k
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Comment: C: Are there downloadable DBs for hotspot mutations?
... adding to the list: 1. database of curated mutations http://docm.genome.wustl.edu 2. civic (mostly clinically actionable) : https://civic.genome.wustl.edu/home ...
written 25 days ago by poisonAlien2.4k
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Comment: C: ABSOLUTE MAF error
... Could be wrong, but I think p in `Start_position` and `End_position` should start with uppercase. `Start_Position ` `End_Position ` ...
written 25 days ago by poisonAlien2.4k
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Comment: C: How to combine expression values of multiple probes for one gene?
... because multiple probesets from a single gene could represent multiple isoforms and by merging them you're loosing this information. ...
written 5 weeks ago by poisonAlien2.4k

Latest awards to poisonAlien

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Popular Question 6 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Appreciated 6 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 6 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 6 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 7 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
Appreciated 7 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 7 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Scholar 7 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Appreciated 11 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 12 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
Scholar 14 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
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
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP

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