Moderator: venu

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venu6.7k
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Posts by venu

<prev • 733 results • page 1 of 74 • next >
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Comment: C: how to extract methylation level of certain genomic regions?
... check out [bedtools intersect][1] function [1]: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ...
written 10 weeks ago by venu6.7k
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Answer: C: genes popup in the volcano plots
... You might want to do a little research on volcano plots, the data used to plot them and x, y axis when you see a volcano plot. Also, google is surprisingly helpful. It took me to following link [which explained][1] > A volcano plot is a type of scatterplot that shows statistical significance (P ...
written 5 months ago by venu6.7k
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Answer: A: How to binarize genomic data
... > How do I find the correct threshold? This can vary for each patient, depending on the heterogeneity in your cohort. IMO, it's hard to find one threshold for all samples/genes. What you can do is - add quartiles to all genes in each patient - Take 3rd and 4th quartiles as 1 and rest 0 for e ...
written 6 months ago by venu6.7k
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Comment: C: Setting Peak Cutoff Using Minimum # of Reads
... That's a usual problem with differential analyses. Along with fold change, use normalized read count (e.g. RPM) as the cut off, e.g. min RPM must be >5. ...
written 6 months ago by venu6.7k
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Comment: C: how to extract mutation from MAF file in python
... `MAF` is already a mutation file. What do you mean by extract mutations? ...
written 7 months ago by venu6.7k
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Comment: C: Split up a matrix into chunks considering the values of a column in Bash
... I'm not providing the code, but here is what you can do prepare a list object where each element of the list contains gene names, e.g. gene_names_list $chunk1 ENSG1 ENSG2 ENSG3 $chunk2 ENSG4 ENSG5 ... Loop over this list object and collect your matrix chun ...
written 8 months ago by venu6.7k
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Comment: C: How do I load a peak file in ChIPseeker?
... May be, by learning basics of R? ...
written 8 months ago by venu6.7k
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Comment: C: How do I load a peak file in ChIPseeker?
... From the docs, if you look at the code files <- getSampleFiles() print(files) `files` is a named list object with paths ti bed file. So you need to create such an object with your files. ...
written 8 months ago by venu6.7k
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Comment: C: Virus Genome Length and GC Content of SARS-COV-2 causing COVID-19
... Hi Dulankak, I'd suggest you add updates within your original thread instead of posting as answer each time when there is a new release. ...
written 8 months ago by venu6.7k
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Answer: A: Have we failed as bioinformatician in this time of COVID-19
... Hi Heididunst, my few points > It about more than 5 months for COVID-19 pandemic but still we far from developing any vaccine If we look at time needed for vaccine development (for previous diseases), one might understand it's not possible to get something reasonable in the span of 1 year, let ...
written 8 months ago by venu6.7k

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Scholar 9 days ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Student 5 weeks ago, asked a question with at least 3 up-votes. For Help a beginner NGS data analyst to face the programming interview
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Appreciated 4 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 5 months ago, created a question with more than 1,000 views. For Human Genome Project: Twenty-five years of big biology
Popular Question 5 months ago, created a question with more than 1,000 views. For Human Genome Project: Twenty-five years of big biology
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
Scholar 5 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Popular Question 5 months ago, created a question with more than 1,000 views. For Human Genome Project: Twenty-five years of big biology
Commentator 6 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
Appreciated 6 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
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
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 8 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Scholar 8 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Commentator 10 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 10 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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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 13 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Good Answer 13 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
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