User: xyang2

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xyang2120
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Posts by xyang2

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Answer: A: Use ChIPpeakAnno to find two-sided nearest genes to a peak
... Julie, You are much helpful. Thanks! I will forward it to people who have similar question. Holly On 12/10/2012 10:46 AM, Zhu, Lihua (Julie) wrote: > Dear Holly, > > I believe that you are interested in finding the peaks that reside in > bi-directional promoters. If so, you can use ...
written 6.7 years ago by xyang2120
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ChIPpeakAnno to find peaks nearest to miRNA
... Hi, Jianrong, Do you think I can use ChIPpeakAnno to get both sided genes for a peak region? If so, how do you suggest, using both the TSS and TTS, or use both the 5UTR and 3UTR? Thanks a lot, Holly ...
chippeakanno written 6.7 years ago by xyang2120 • updated 22 months ago by jun.yu0
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Comment: C: A basic question about retrieve the absolute genome position from the output of
... Paul, Your demon is much clear for a beginner. Thanks a lot. Talking back for searching putative binding site, when you say " Another thing to keep in mind here is something suggested by Steve a couple of weeks ago: it may be better to think in terms of proximal regulatory regions, a full 5000 bp u ...
written 6.8 years ago by xyang2120
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Comment: C: A basic question about retrieve the absolute genome position from the output of
... Steve, As the motif I am interested is [AAGTTTAA]. Then I got a result on the negative strand as chr3:49450073-49450080, [GGTGAGGC], which is reversely complementary to [AAGCCTCA]. Should I compare the reversely complementary hit to the motif? If a hit is on a positive strand, then to compare the ...
written 6.8 years ago by xyang2120
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Comment: C: A basic question about retrieve the absolute genome position from the output of
... Hi, Steve, I should pay attention to the arrows near the gene RHOA, e.g. chr3:49,396,579-49,449,428. Yes, left and right are relatively. "people often/occasionally/might-be-inclined-to include sequence up to and including the first intron of a gene when looking for regulatory motifs" - If you have ...
written 6.8 years ago by xyang2120
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Comment: C: A basic question about retrieve the absolute genome position from the output of
... Hi, Steve, Thank you. 49449428+999-354 =49450073 49449428+999-347= 49450080 By searching chr3:49450073-49450080 I got [GGTGAGGC], which is reversely complementary to [AAGCCTCA] as expected. > reverseComplement(DNAString("GGTGAGGC")) 8-letter "DNAString" instance seq: CAGCCTCA More qu ...
written 6.8 years ago by xyang2120
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A basic question about retrieve the absolute genome position from the output of of function matchPWM .
... Dear all, I am learning how to "Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching" from the Bioconductor online help file at http://www.bioconductor.org/help/workflows/gene-regulation-tfbs/ When I ran the following codes, I can not match the results back to the U ...
written 6.8 years ago by xyang2120 • updated 6.8 years ago by Steve Lianoglou12k
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Comment: C: more question about makeVennDiagram
... Julie, Yes, it works now. Thanks a lot, Holly On 8/1/2012 9:33 AM, Zhu, Lihua (Julie) wrote: > Re: more question about makeVennDiagram Holly, > > Looks like you created your peaks without assigning names for each > range. The helper function BED2RangedData or GFF2RangedData > automat ...
written 7.1 years ago by xyang2120
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Answer: A: more question about makeVennDiagram
... Julie, I think the release may not be the issue. The Bioconductor 2.10 is designed for R2.15. I installed the package within R as following: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.7, ?biocLite for help > biocLite("ChIPpeakAnno") BioC_mirror: http://bio ...
written 7.1 years ago by xyang2120
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Comment: C: Help - Rgraphviz install error for R 2.15 on Ubuntu 11.10
... Thanks Dan. It works now. Holly On 04/06/2012 07:09 PM, Dan Tenenbaum wrote: > Hi Holly, > > > On Fri, Apr 6, 2012 at 1:20 PM, Holly wrote: >> Hi, >> >> I recently reinstall my machine and cannot figure out how to make Rgraphviz >> work. Following is the informat ...
written 7.4 years ago by xyang2120

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