User: learnerforever

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Posts by learnerforever

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Comment: C: Selecting Gene Subsets Such That No Two Genes Occur In The Same Set More Than "T
... Thanks, but I would also appreciate some explanation of your solution. How did you arrive at this? ...
written 6.0 years ago by learnerforever520
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Selecting Gene Subsets Such That No Two Genes Occur In The Same Set More Than "T" Times
... In one of my gene sets, I am interested in selecting gene subsets such that no two genes occur in the same set more than "t" times. Mathematically, given n objects and selecting k objects without replacement, how many combinations exist such that no two objects are in the same group more than "t" ti ...
gene written 6.0 years ago by learnerforever520 • updated 6.0 years ago by KCC3.9k
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Comment: C: Sample Size For Tumor Normal Ngs Study
... This was very useful! Is there any similar work/calculator for paired tumor-normal analysis and detecting somatic rather than inherited mutations? ...
written 6.0 years ago by learnerforever520
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Sample Size For Tumor Normal Ngs Study
... In a recent paper http://genesdev.cshlp.org/content/25/6/534.long It has been quoted that for exome-sequencing "it was calculated that 500 tumor samples are needed to detect, with ∼80% power, genes that are mutated in 3% of patients (assuming a typical background mutation rate)" The reference cit ...
statistics written 6.0 years ago by learnerforever520 • updated 6.0 years ago by Neilfws48k
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Ion Variant Hunter
... Has anyone used stand-alone Variant calling tools Ion Variant Hunter on Torrent generated BAMs? https://github.com/iontorrent/Ion-Variant-Hunter Could you please post command line parameters used? Thanks! ...
ion-torrent written 6.6 years ago by learnerforever520
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How To Convert Uniprot Ids To Ensemble Gene/Transcript Ids
... I have ~3000 UNIPROT IDs and some of them have "-", that I'm guessing are some sort of isoforms. A0AVT1 A0FGR8-4 A0M8Q6 A0MZ66-2 A1L0T0 A1L4H1-2 A1X283 A2A2D0 A2A2Z9 A2ACR1 What's the most reliable way to convert these to corresponding ENSEMBL gene/transcript IDs? I used biomart but hyphens faile ...
uniprot written 6.6 years ago by learnerforever520 • updated 6.6 years ago by Jerven640
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Answer: A: Deseq High Within Group Dispersion
... Thanks, Jeremy. Size factors for the raw read counts were: 2.08 1.16 0.59 1.36 0.73 1.37 1.29 1.19 0.02 0.95 1.28 1.31 0.55 1.97 1.57 2.08 2.26 1.47 0.78 1.53 0.76 0.95 After size factor normalization, I got rid of low counts at 40% (use <- (rs > quantile(rs, 0.4)) as shown in the manual. Th ...
written 6.8 years ago by learnerforever520
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Deseq High Within Group Dispersion
... Hi guys, I have posted a question and images on seqanswers http://seqanswers.com/forums/showthread.php?t=21723 and was hoping someone here might have a few ideas. Thanks! ...
deseq rna-seq written 6.8 years ago by learnerforever520
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Polyphen-2 Classifier Model
... On the polyphen-2 webpage http://genetics.bwh.harvard.edu/pph2/bgi.shtml There are two options for the classifier model: HumDiv HumVar Could anyone explain what these are? Is there a documentation for this? Thanks, forum. ...
written 7.0 years ago by learnerforever520 • updated 7.0 years ago by Pierre Lindenbaum120k
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1000 Genomes Variants In Ucsc Browser
... Is it possible to view 1000 genomes variants in ucsc hg19 genome browser? If yes, which track should be enabled? ...
1000genomes ucsc written 7.0 years ago by learnerforever520 • updated 6.8 years ago by Giovanni M Dall'Olio26k

Latest awards to learnerforever

Appreciated 6.6 years ago, created a post with more than 5 votes. For How To Convert Uniprot Ids To Ensemble Gene/Transcript Ids
Student 6.6 years ago, asked a question with at least 3 up-votes. For How To Convert Uniprot Ids To Ensemble Gene/Transcript Ids
Student 7.0 years ago, asked a question with at least 3 up-votes. For 1000 Genomes Variants In Ucsc Browser
Student 7.1 years ago, asked a question with at least 3 up-votes. For Reference Bias In Alignments
Student 7.1 years ago, asked a question with at least 3 up-votes. For Rna-Seq Data Variant Calling
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Rna-Seq Data Variant Calling
Student 7.2 years ago, asked a question with at least 3 up-votes. For Visualizing Fpkm In Igv
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Vdb Field In Samtools
Student 7.6 years ago, asked a question with at least 3 up-votes. For Chimerascan Rna-Seq Fusion Tool
Appreciated 7.6 years ago, created a post with more than 5 votes. For Complex Genomic Regions
Student 7.6 years ago, asked a question with at least 3 up-votes. For Complex Genomic Regions
Student 7.7 years ago, asked a question with at least 3 up-votes. For Rna-Seq Within Group Variability
Student 7.7 years ago, asked a question with at least 3 up-votes. For Assembly Of Unmapped Reads
Student 7.7 years ago, asked a question with at least 3 up-votes. For Repeated Rsids In Dbsnp?
Popular Question 7.7 years ago, created a question with more than 1,000 views. For Repeated Rsids In Dbsnp?

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