User: poisonAlien
poisonAlien • 2.4k
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Cancer genomics
Posts by poisonAlien
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... Try [lncRNA-screen][1]
[1]: https://github.com/NYU-BFX/lncRNA-screen ...
written 1 day ago by
poisonAlien • 2.4k
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... 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 ...
written 2 days ago by
poisonAlien • 2.4k
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... 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
poisonAlien • 2.4k
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... how did you look at TCGA cnv data? Was it from GISTIC output ? ...
written 21 days ago by
poisonAlien • 2.4k
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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
poisonAlien • 2.4k
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170
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... 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
poisonAlien • 2.4k
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200
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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
poisonAlien • 2.4k
1
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204
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... 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
poisonAlien • 2.4k
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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
poisonAlien • 2.4k
1
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1.7k
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... 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
poisonAlien • 2.4k
Latest awards to poisonAlien
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?
Popular Question
6 months ago,
created a question with more than 1,000 views.
For questions on rna-seq data analysis
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 ?
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?
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?
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?
Commentator
17 months ago,
created a comment with at least 3 up-votes.
For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
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