Moderator: venu

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venu6.0k
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https://itsvenu.github...
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Posts by venu

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Comment: C: History of Biostars
... I'd guess, many basic questions are being asked over the previous years and answered very well, so with a simple google search, first hits are landing on biostars threads. Also *many* tool developers are documenting their tools with clean examples and responding to the user queries. Might be saturat ...
written 22 days ago by venu6.0k
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Comment: C: History of Biostars
... Aw, your title makes more sense. Yes, I will try to make per-year frequency of tags (a good idea to see troubled topics per year :p). ...
written 22 days ago by venu6.0k
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Comment: C: History of Biostars
... Thanks Vijay. It may makes sense to get an overview of Tools per year, to check how frequently new tools are being developed. But what do you mean by `with application`? Because, each tool is flagged with more than one tag, so it's extremely complicated to get one-word application to each tool (by p ...
written 22 days ago by venu6.0k
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Comment: C: History of Biostars
... Thanks Wouter. Do you mean, fraction of change compared to previous year or something else? This is a type of analysis I thought of but didn't do *yet*. ...
written 22 days ago by venu6.0k
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Blog: Evolution of Biostars
... Hi, I have been *planning* to do this small data science project & finally got sometime to *actually do* it. I scraped `Biostars` data (Question title, day asked & associated tags) since the site is live until today (2009 - 23/02/2019) and asked some questions. Here is the brief overview ...
biostars blog written 22 days ago by venu6.0k • updated 21 days ago by JC7.6k
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Comment: C: Pseudotime on scRNAseq TPMs?
... [This page][1] listed all pseudotime analysis algorithms. Worth exploring to check if any of these can do the job you want? [1]: https://github.com/agitter/single-cell-pseudotime ...
written 28 days ago by venu6.0k
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Comment: C: Chip seq (ac) reads count per pick
... Check [deepTools multiBamSummary][1] [1]: https://deeptools.readthedocs.io/en/develop/content/tools/multiBamSummary.html ...
written 5 weeks ago by venu6.0k
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Comment: C: Help with HOMER motif profile plots
... I created a bigiwg ( using bedtools genomecov + kent utils) and plotted with plotProfile. The motif I'm interested in is has very sparse hits, applying loess fit on plotProfile output data is more/less looking closer to the above plot. I think I understood what's happening inside. ...
written 5 weeks ago by venu6.0k
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Answer: A: Help with HOMER motif profile plots
... For future googlers, here is the response from lead author of HOMER, Chris Benner > The motif plots are normalized by taking the actual motif totals, then normalizing by the bin size used in the histogram (so that the motif densities are comparable across different bin sizes) and the total numbe ...
written 5 weeks ago by venu6.0k
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Help with HOMER motif profile plots
... Hi, I'm trying to understand profile plots for motifs. Homer has a function (annotatePeaks.pl) to generate motif density profiles that looks like following (lifted from [here][1]) ![enter image description here][2] While I understand what these profile plots convey for ChIP-seq data (e.g. those g ...
homer motifs written 5 weeks ago by venu6.0k

Latest awards to venu

Appreciated 22 days ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Help needed with selecting top DE genes, Microarray data analysed with "limma"
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 4 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Great Question 4 months ago, created a question with more than 5,000 views. For covert STOCKHOLM alignment to FASTA alignment
Popular Question 4 months ago, created a question with more than 1,000 views. For Help needed with selecting top DE genes, Microarray data analysed with "limma"
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: perl code to extract sequences from multi-line fasta works on all test files but
Popular Question 6 months ago, created a question with more than 1,000 views. For Help needed with selecting top DE genes, Microarray data analysed with "limma"
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: perl code to extract sequences from multi-line fasta works on all test files but
Appreciated 6 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Popular Question 7 months ago, created a question with more than 1,000 views. For Assemble short reads based on k-mers
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Popular Question 7 months ago, created a question with more than 1,000 views. For Map a protein domain information to a sequence
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Popular Question 8 months ago, created a question with more than 1,000 views. For Map a protein domain information to a sequence
Scholar 8 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Scholar 9 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS

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