User: The

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The160
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Posts by The

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Dendrogram line width in heatmap.2
... Hi, Is there anyway to control the dendrogram line thickness in heatmap.2() function? This is how one can do that in pheatmap(). I'm looking for something similar in heatmap.2 [pheatmp dendrogram line width control ][1] [1]: https://stackoverflow.com/questions/50469883/change-line-width-of-de ...
R dendrogram lwd heatmap.2 heatmap written 7 weeks ago by The160
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Answer: A: Transform log2 fold changes in z-scores
... What I believe there is not sufficient 'scatter' in the plot. In your case the p-value is usually better(lower) with increase in absolute(fold change) almost monotonically . That might have to do something with the calculation of p-value in Rank Product analysis( do they still calculate it by ran ...
written 11 weeks ago by The160
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Answer: A: Extracting important gene with similar expression level from multiple samples
... How about selecting genes with least variance across samples? Otherwise some clustering will give you genes with similar expressions ...
written 11 weeks ago by The160
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Answer: A: Secondary Structure Alignment Method
... If I correctly remember , there was a paper in PNAS by George D Rose in late 90s which dealt with this. The goal was to find out structurally similar sequences based on predicted secondary structure. So far I remember they employed a simple scoring system (match/mismatch binary type): ![enter imag ...
written 11 weeks ago by The160
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Comment: C: How to "linearize" or "unfold" a PDB format structure to secondary structure?
... yes, as Michael wants to preserve the well defined secondary structure elements ...
written 12 weeks ago by The160
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Answer: A: How to "linearize" or "unfold" a PDB format structure to secondary structure?
... Can this help, with default values? I guess it outputs the model in PDB format as well "We set the default for the backbone dihedral angles to the extended conformation (ϕ = −120∘, ψ = 140∘, ω = 180∘)." [PeptideBuilder: A simple Python library to generate model peptides][1] [Github repository][2] ...
written 12 weeks ago by The160
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Comment: C: Convert a two-column file to a single file with interlayed rows
... No problem for Notepad++, you can convert EOLs to unix style '\n' to windows '\r\n' and vice versa, under the EDIT-> EOL Conversion menu ...
written 3 months ago by The160
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Answer: A: Convert a two-column file to a single file with interlayed rows
... For this type of simple conversion , I would use regex based find-and-replace features of text editors like Notepad++, provided the file is not too big for the editor to open . ![Notepad++ Regex][1] [1]: https://i.ibb.co/0V3VpyT/fasta-Convert.png ...
written 3 months ago by The160
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Answer: A: Get identical elements and index from 2 Arrays in Perl
... use strict; use warnings; my @A = ("Red", "Green", "Yellow"); my @B = ("Yellow", "Black","Yellow","Red", "White", "Yellow"); foreach my $col (@A){ my @hit_indices = map{$B[$_] eq $col ? $_: () }(0..$#B); scalar(@hit_indices) ? print $col, " at indices ",join(',',@hit ...
written 3 months ago by The160
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Forum: Good books on application of Machine Learning in Bioinformatics
... Hello all, I'm looking for books on applications of machine learning and statistical data mining in bioinformatics with example codes provided in R and/or python. I came across the following two books: the first being a quite good one, provides the code in MATLAB, which i'm not very comfortable wi ...
bioinformatics forum book machine learning written 3 months ago by The160

Latest awards to The

Popular Question 6 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 8 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 8 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 9 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 19 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Epic Question 20 months ago, created a question with more than 10,000 views. For R: Scaling the rows of a matrix
Popular Question 21 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 21 months ago, created a question with more than 1,000 views. For Distance between two gene sets
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Popular Question 2.9 years ago, created a question with more than 1,000 views. For Distance between two gene sets
Great Question 3.0 years ago, created a question with more than 5,000 views. For R: Scaling the rows of a matrix
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Fisher'S Exact Test For Gene Rank Enrichment
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Using Perl Text::Wrap For Wrapping Text
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Fisher'S Exact Test For Gene Rank Enrichment
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Scholar 4.6 years ago, created an answer that has been accepted. For A: Mapping multiple expression data on KEGG genes and metabolites

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