Moderator: venu

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venu5.6k
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Posts by venu

<prev • 672 results • page 1 of 68 • next >
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Comment: C: ClusterProfiler cannot map any gene
... Try converting your ids to entrez ids as in the clusterProfiler manual [here][1] using `bitr` function. I think this tools doesn't work with gene symbols. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#bitr-biological-id-translator ...
written 2 days ago by venu5.6k
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Comment: C: Netheat in R for network meta-analysis
... This might help: [Error in .External.graphics R][1] [1]: https://stackoverflow.com/questions/18350353/error-in-external-graphics-r ...
written 7 days ago by venu5.6k
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Comment: C: Gene enrichment analysis
... May be, you can define 'better'. People will understand quickly. ...
written 8 days ago by venu5.6k
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Answer: A: Why learn programming in bioinformatics?
... This might not qualify as an answer, however I'm tempted to write one as something similar discussion happened today. A guy sitting next to me is a pro (good) in excel. I'm not (but I'm good at some scripting and command line tools). This guy said excel is easy to calculate some basic number like ...
written 16 days ago by venu5.6k
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Comment: C: Correlation of TF Binding with expression data
... > if you have multiple TFBS to one gene and how would you correlate each binding site with expression across multiple condition It's not a problem unless TFBS are overlapping themselves. I don't know what is your actual goal. But I would simply do each TFBS to GENE correlation and take the highe ...
written 5 weeks ago by venu5.6k
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Answer: A: Correlation of TF Binding with expression data
... Do you have TF ChIP-seq data or Histone ChIP-seq data and potential TF binding sites? Since you did not mention about that, I would assume you have TF ChIP-seq data, one direct approach would be, 1. Assign each peak/TFBS to nearest 1 or 2 genes (1 upstream and 1 downstream of peak) 2. Calculate ...
written 5 weeks ago by venu5.6k
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Answer: A: Is possible to quantify the RNAPOLII levels on all the annotated genes using biw
... It's good that you already have bigwig files. Take bed file of annotated genes and use deepTools function [multiBigwigSummary][1]. If you want to plot a metagene plot of RNApolII level over the gene, they also have functions like `computeMatrix` and `plotProfile`. If you have plans to plot, make su ...
written 5 weeks ago by venu5.6k
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Comment: C: Most important International Big Data Projects: Genetics and Epigenetics
... What about TCGA? P.S. A one line description of what type of data one can find in each of the project would be helpful. ...
written 6 weeks ago by venu5.6k
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Comment: C: Enrichment Analysis in R
... There is so called `vignettes/manual/docuemntation` for every R/Bioconductor package. You can find use cases in there. ...
written 6 weeks ago by venu5.6k
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Comment: C: Bioconductor: ALL dataset, correct syntax using the exprs call?
... There is no glaring problem but an obvious one. `exprs(ALL)` This returns a matrix. `min` and `max` functions are returning the lowest and highest value from that matrix. I'm not sure if `age` column presents in a expressionSet object (my best guess is not). You just have columns - samples, rows-g ...
written 6 weeks ago by venu5.6k

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Popular Question 2 days 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 15 days 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 16 days ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Assemble short reads based on k-mers
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Map a protein domain information to a sequence
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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Map a protein domain information to a sequence
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
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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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
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
Appreciated 4 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 4 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
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
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
Popular Question 7 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
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 Sequence extraction from PFAM db with accession ID

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