User: Ashley
Ashley • 50
- Reputation:
- 50
- Status:
- Trusted
- Location:
- China
- Twitter:
- ashley199305
- Last seen:
- 2 days, 14 hours ago
- Joined:
- 3 years, 7 months ago
- Email:
- l***********@gmail.com
Posts by Ashley
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... Thank you very much. ...
written 4 weeks ago by
Ashley • 50
0
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2
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107
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Answer:
A: How Can I Merge Intervals ?
... I know how to calculate this one. Just using groupby function and pd object.
df.groupby(col2 and col3).apply(lambda x: np.average(col7, weights=col8)) ...
written 11 weeks ago by
Ashley • 50
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Answer:
A: How Can I Merge Intervals ?
... I think pandas and numpy models are suit for our analysis. ...
written 11 weeks ago by
Ashley • 50
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... I want to merge intervals using weighted means instead of sum or average.
Thanks for taking your time to read this file.
My input data:
data format: chrFileA startFileA endFile1 chrFile2 startFile2 endFile2 value TheLengthOfOverlap
chr1 12000 13000 chr1 1298 ...
written 11 weeks ago by
Ashley • 50
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... ![my example is:][1] (original link: https://www.dropbox.com/s/h8de0hcc8vc193t/data.jpg?dl=0 )
[1]: https://ucec75035bc491864dd23f9f514e.previews.dropboxusercontent.com/p/thumb/AAWM3Y5PRY16HjGCuFMaUrWBTLH_Mcdpo6T8NvJvTGzG_0_AayTbA96F-d2vRAo2aZwtb-0OYf9M3gekXhc1_ifFGLapSZVA6VdgseiFecVmf1Y8deKVQg3U ...
written 5 months ago by
Ashley • 50
• updated
3 months ago by
Devon Ryan ♦ 90k
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... 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 months ago by
Ashley • 50
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... > 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 months ago by
Ashley • 50
1
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... 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 ...
0
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159
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... 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 5 months ago by
Ashley • 50
0
votes
1
answer
159
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1
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... [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 ...
written 5 months ago by
Ashley • 50
Latest awards to Ashley
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6 weeks ago,
created a question with more than 1,000 views.
For Gene set enrichment analysis (GSEA) of some lncRNAs(known for Gencode and newly assembled)
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How to calculate "Tissue specificity score" using JSD
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5 months ago,
created an answer that has been accepted.
For C: Questions About How to Plot NOMe-seq Plot
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10 months ago,
created a question with more than 1,000 views.
For How to calculate "Tissue specificity score" using JSD
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23 months ago,
created a question with more than 1,000 views.
For Gene set enrichment analysis (GSEA) of some lncRNAs(known for Gencode and newly assembled)
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