User: venu

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venu4.6k
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Germany
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https://venuthatikonda...
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nerd_yie
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Posts by venu

<prev • 594 results • page 1 of 60 • next >
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Comment: C: Unable to locate package tcc:i386
... That means the package `tcc:i386` is not in official Ubuntu repository. Which Ubuntu release are you using? ...
written 4 hours ago by venu4.6k
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Comment: C: Problem with downloading cancer data
... Do you have anything under `/icgc` directory ? `ls /icgc` ? ...
written 1 day ago by venu4.6k
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Comment: C: What file formats requires for WGCNA ??
... Did you check their manual/tutorial page [here][1] ? [1]: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html ...
written 1 day ago by venu4.6k
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Comment: C: nearby genes expression
... Both of them takes <5 min to complete the task. I can't think of any other shortcut. ...
written 4 days ago by venu4.6k
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Comment: C: nearby genes expression
... Sure. 1. Get the coordinates of your gene of interest from GTF. 2. use bedtools to find what are the nearest genes using `closest` feature 3. Take the gene IDs from step.2 and `grep` for `log2FC` from DESeq2 results or 1. Go to UCSC genome browser and enter your gene of interest 2. Zoom out ...
written 5 days ago by venu4.6k
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Comment: C: ChIP-Seq Intensity Analysis
... @solveforj, I have successfully used `deeptools` for similar purpose. I was using the term `re-quantifiation` for this analysis. Briefly, you can do this, 1. Generate normalized `bigwig` files from `bam` with `bamCoverage` function 2. Call peaks using `MACS` on the data for which you want to gen ...
written 7 weeks ago by venu4.6k
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Comment: C: ChIP-Seq Intensity Analysis
... Providing few more details would help to answer. Like, why do you want to measure intensity in bins, for differential analysis or just to check comparative signal in different bins/regions. You can use `bedtools`, `deeptools`..etc to calculate intensity/read count and normalize the values. ...
written 7 weeks ago by venu4.6k
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Comment: C: Making UpSetR plot with title
... +1. I use `convert` mostly to conver `PDF` to `HQ PNG` format. This is completely new to me. Thanks. ...
written 8 weeks ago by venu4.6k
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Comment: C: Making UpSetR plot with title
... From their reference manual [here][1], it seems there is no argument to add a `title` to the plot. (you can check one more time just in case if I missed it) [1]: https://cran.rstudio.com/web/packages/UpSetR/UpSetR.pdf ...
written 8 weeks ago by venu4.6k
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Comment: C: How to add column to a file from from another file having one common column but
... You don't need to add anything extra while posting some example data. Just paste few lines as it is and just mention it is a tab / space separated file. ...
written 8 weeks ago by venu4.6k

Latest awards to venu

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Appreciated 5 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
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
Scholar 7 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Scholar 7 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Scholar 7 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
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
Commentator 8 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 9 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
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
Scholar 13 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
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
Scholar 14 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Appreciated 14 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 14 months ago, created a question with more than 1,000 views. For covert STOCKHOLM alignment to FASTA alignment
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Student 15 months ago, asked a question with at least 3 up-votes. For Help a beginner NGS data analyst to face the programming interview

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