User: Ashley

gravatar for Ashley
Ashley40
Reputation:
40
Status:
New User
Location:
China
Twitter:
ashley199305
Last seen:
1 month ago
Joined:
3 years, 3 months ago
Email:
l***********@gmail.com

Posts by Ashley

<prev • 58 results • page 1 of 6 • next >
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Comment: A: How to calculate dinucleotide A/T patterns in a given human reference genome reg
... ![my example is:][1] [1]: https://www.dropbox.com/s/h8de0hcc8vc193t/data.jpg?dl=0 ...
written 5 weeks ago by Ashley40
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Comment: C: How to calculate dinucleotide A/T patterns in a given human reference genome reg
... For our example, > consensusMatrix(dinucleotideFrequency(DNA.set)) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] 0 2 3 2 2 3 1 0 0 2 0 3 1 0 0 2 1 1 0 0 1 3 1 1 ...
written 5 weeks ago by Ashley40
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Comment: C: How to calculate dinucleotide A/T patterns in a given human reference genome reg
... > dinucleotideFrequency(DNA.set) AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT [1,] 2 0 1 1 0 1 2 1 1 1 1 2 1 3 1 1 [2,] 0 2 2 1 2 2 1 1 1 1 0 1 2 1 1 1 [3,] 2 2 0 0 1 0 2 2 0 1 3 2 1 1 2 0 [4,] 0 0 0 1 0 5 1 5 ...
written 5 weeks ago by Ashley40
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How to calculate dinucleotide A/T patterns in a given human reference genome region?
... library("Biostrings") I want to calculate the probability of di-nucleotide AA, TT, AT, and TA in each 2 location. My DNA sequence is as follows: DNA.set A DNAStringSet instance of length 5 width seq names ...
R sequence written 5 weeks ago by Ashley40
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Answer: A: How to compute the mono-nucleotide position specific frequency matrix and plot f
... In fact, I obtained the x-axis. However, I don't know how to construct the position specific frequency matrix (PSFM). The details are as follows: [enter link description here][1] [1]: https://www.dropbox.com/s/5bmnkbrf0aja705/PSFM.jpg?dl=0 But I couldn't understand it's meaning. ...
written 6 weeks ago by Ashley40
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How to compute the mono-nucleotide position specific frequency matrix and plot for it
... [enter link description here][1] [1]: https://www.dropbox.com/s/93oc61m107bl174/Fig.jpg?dl=0 The figure comes from the paper (Fig.1): https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000834 The x-axis represents for the dyad's location (the middle of nuclesome), while ...
mnase-seq nuclosome written 6 weeks ago by Ashley40
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Answer: A: eCLIP peak calling
... Hi, I think Piranha is also a good strategy for analyzing CLIP-seq data. You can download from: http://smithlabresearch.org/software/piranha/ Thanks. Ashley ...
written 6 weeks ago by Ashley40
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Comment: C: Questions About How to Plot NOMe-seq Plot
... Thank you very much for your kind email and reply. ...
written 7 weeks ago by Ashley40
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Comment: C: Questions About How to Plot NOMe-seq Plot
... Thanks for your quick reply. I don't want to delete the entire thread. I just want to close this thread because the answer is provided. Thanks a lot. ...
written 7 weeks ago by Ashley40
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Comment: C: Questions About How to Plot NOMe-seq Plot
... I want to close this thread. It's Okay now. human genome version hg18 and hg19 ...
written 7 weeks ago by Ashley40

Latest awards to Ashley

Scholar 7 weeks ago, created an answer that has been accepted. For C: Questions About How to Plot NOMe-seq Plot
Popular Question 6 months ago, created a question with more than 1,000 views. For How to calculate "Tissue specificity score" using JSD

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