User: venu

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venu5.1k
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Posts by venu

<prev • 640 results • page 1 of 64 • next >
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Comment: C: Conference/Symposium/Seminar/Workshop alert 2018-2019
... [This might help][1]. [1]: http://generegulation.info/index.php/conferences-meetings-schools/conferences-2018 ...
written 4 days ago by venu5.1k
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Comment: C: getting a combination of all predicted genes
... I do not know anything about these predictors and their output format. But I can certainly say `BED`tools will not work on them (most of the `BED`tools functions require `BED` regions to work). From what I understand from your example, you just need union of all results? `cat MGA_results.txt GEN ...
written 4 days ago by venu5.1k
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Answer: C: Merging specific columns from different txt files in a unit file
... FYI, featureCounts accepts many bam files at once and generates one count table for all BAMs. Regarding your error, I think that's not the proper way to use `join`. I guess order of genes will be same in all counts.txt files from featureCounts. You can simply do `paste *counts.txt` with little prep ...
written 10 days ago by venu5.1k • updated 10 days ago by h.mon15k
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Comment: C: How to just add some selected gene names to a volcano plot
... Check [these examples][1]. [1]: https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html ...
written 14 days ago by venu5.1k
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Answer: C: How to just add some selected gene names to a volcano plot
... Change this line of code data <- read.table("trans.counts.matrix.J_vs_M.edgeR.DE_results", header=TRUE) to data <- read.delim("trans.counts.matrix.J_vs_M.edgeR.DE_results", header=TRUE, na.strings=c("","NA")) This adds `` to empty cells which will be ignored in the plot and only ge ...
written 14 days ago by venu5.1k
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Comment: C: Volcano plot help code
... One more: [Repel overlapping text labels in ggplot2][1] [1]: http://www.gettinggeneticsdone.com/2016/01/repel-overlapping-text-labels-in-ggplot2.html ...
written 5 weeks ago by venu5.1k
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Comment: C: Comparing gene expression overlap with hypergeometric distribution
... There also exists a Bioconductor package for these type of tests, [GeneOverlap][1] [1]: https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html ...
written 6 weeks ago by venu5.1k
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Comment: C: FIMO output to bed
... Try this cat fimo_result.txt | grep -v motif_alt_id | cut -f3 | tr ':-' '\t' | sort -k1,1V -k2,2n > fimo_to_bed.bed ...
written 6 weeks ago by venu5.1k
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Comment: C: Merging list of bam files with samtools merge
... I don't see python code in your example. ...
written 7 weeks ago by venu5.1k
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Answer: A: find transcription factors in a list of genes
... [Enrichr][1] Input your gene list there and select required results. I strongly remember it give what you want. [1]: http://amp.pharm.mssm.edu/Enrichr/ ...
written 8 weeks ago by venu5.1k

Latest awards to venu

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 10 days ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Appreciated 14 days ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 24 days ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Commentator 11 weeks 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 3 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Commentator 3 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 3 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
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
Scholar 4 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Commentator 5 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 5 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 Sequence extraction from PFAM db with accession ID
Popular Question 6 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Popular Question 7 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Appreciated 10 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
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

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