User: roy.granit
roy.granit • 830
- Reputation:
- 830
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- Location:
- Israel/LabWorm
- Website:
- http://roygranit.me/
- Twitter:
- rgranit
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- Last seen:
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- Joined:
- 6 years, 1 month ago
- Email:
- r*********@gmail.com
I'm a co-founder & CTO at LabWorm a crowd voting platform that enables scientists to discover the best & newest online research tools. Previously I explored pathways that determine intratumoral heterogeneity using high-throughput molecular biology & bioinformatics. My personal website.
Posts by roy.granit
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C: Interpreting DEseq2 output
... Thanks, using `counts(dds, normalized=TRUE)` I was indeed able to obtain the normalized counts and obtain a better understanding of the data.. ...
written 9 weeks ago by
roy.granit • 830
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C: Interpreting DEseq2 output
... The lib is 3' based, so I believe that the transcript length is not relevant in this case ...
written 9 weeks ago by
roy.granit • 830
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... I have been using DEseq2 for quite a while, but today I was looking a certain transcript and compared that to the raw counts, and found little login in the results. These are the output values:
log2FoldChange: 0.3434941483
pvalue: 2.16740140052804e-06
padj: 5.65192536063831e-06
...
written 9 weeks ago by
roy.granit • 830
• updated
9 weeks ago by
rpolicastro • 2.1k
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... Thanks, how reliable is bbmap? never heard of it.. ...
written 4 months ago by
roy.granit • 830
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... I did not mention that some of these genes do not exist in the genome.. ...
written 4 months ago by
roy.granit • 830
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... I have 3 amplicons that I have sequenced and now I wish to align them to the sequences of these three genes so I can quantify how many reads mapped to each gene.
In order to use STAR must I go through the steps of genome indexing or is there a way to align stright with the fasta file containing the ...
written 4 months ago by
roy.granit • 830
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... I have a human DNA sequence and I wish to check how variable this sequence is.. is there a way to check how many SNPs are found at the given location?
Thanks! ...
written 5 months ago by
roy.granit • 830
• updated
5 months ago by
Pierre Lindenbaum ♦ 131k
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... I wish to know if the overlap of ALL three lists together is significant, so I don't believe that contingency table would fit this use case. ...
written 6 months ago by
roy.granit • 830
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... Hi All,
I have 3 independent lists of genes, and I would like to assess the statistical significance of the intersection of the lists. For two groups I have used hypergeometric test, but I'm uncertain what should be done here.
Any ideas?
Thanks! ...
written 6 months ago by
roy.granit • 830
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Comment:
C: ChIP to genes
... I found these tools: http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html and http://great.stanford.edu/public/html/ ...
written 6 months ago by
roy.granit • 830
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