Moderator: venu

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venu5.7k
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Posts by venu

<prev • 684 results • page 1 of 69 • next >
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Comment: C: Plot normalized counts DESeq or TPM?
... In an ideal case (any case?), your differential genes from DESeq2 should show same pattern when you plot a box/violin plot with TPMs. Meaning, over expressed genes should show high TPMs and vice versa. But I would once check the clustering heatmap produced by VST counts and TPMs. If the clusters ar ...
written 7 days ago by venu5.7k
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Comment: C: Calculate Tag density
... May be you have to look up definition of tag count one more time. Check this: [ChIP seq basic terminology: what is a ChIP-seq tag?][1] > plot the tag density for a certain group of genes What do you mean by plotting? If you want to visualise ChIP enrichment over some genes, you can use `IGV` o ...
written 11 days ago by venu5.7k
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Comment: C: Calculate Tag density
... The details are not sufficient to suggest a workflow or tool. You could try to explain in detail what your goal is. That being said, if you have a bed file with gene coordinates and BAM file, there are number of tools to calculate raw read/tag density and normalized read density. E.g. `deeptools`, ...
written 11 days ago by venu5.7k
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Comment: C: plot with ggplot2
... Can you show `head(df1`) & `head(df2)`? Seems like you can add add one more column to each `data.frame` e.g. df1$SOURCE <- "df1" df2$SOURCE <- "df2" model_3 = rbind(df1, df2) .... Then color based on `SOURCE` ...
written 12 days ago by venu5.7k
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Comment: C: NMF not working for identifying mutational signature
... > I am not able to compare my mutational catalogue with COSMIC 30. And that is exactly what I'd like to do. If that is what all you want to do, check YAPSA package. It has functions to calculate exposures for known COSMIC signatures. You can also specify cut-offs e.g. a signature must be reporte ...
written 25 days ago by venu5.7k
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Answer: C: NMF not working for identifying mutational signature
... Sorry to disappoint you but it's not that simple. NMF is a good approach for mutational signatures but where did you see that approach/tutorial? You need a reference set of signatures (COSMIC 30 or PCAWG 60, google it) and a mutational catalogue (the matrix you have now). There are several establi ...
written 26 days ago by venu5.7k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... Thanks. I will definitely check the log2 normalized counts. ...
written 5 weeks ago by venu5.7k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... Yes, by merging, what I meant is basically adding some peaks from panel B to panel A. - From standard analysis, that is already significant (and also tested experimentally). - This is a good question. We can't produce biological replicates (because of the lack of different models with same genet ...
written 5 weeks ago by venu5.7k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... I was also thinking of lowering qvalue cut off (I've used 0.01). Co-occupancy is one of the strongest point for whole work, that's why I am trying not to loose any of the sites/genes which show actual signal. Do you have any comments on the points I mentioned in the main question about merging based ...
written 5 weeks ago by venu5.7k
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Comment: C: Does it make sense to consider a genomic loci when there is no peak but high sig
... Hi Jared, thanks for the answer. One more thing I didn't mention is - We do not have replicates (I know :( ) - The figures shown are actually from the differential results of [`MAnorm`](https://github.com/shao-lab/MAnorm) MAnorm produced these regions as not significantly different before and ...
written 5 weeks ago by venu5.7k

Latest awards to venu

Scholar 3 days ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Great Question 12 days ago, created a question with more than 5,000 views. For covert STOCKHOLM alignment to FASTA alignment
Popular Question 21 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 4 weeks 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 8 weeks ago, created a question with more than 1,000 views. For Help needed with selecting top DE genes, Microarray data analysed with "limma"
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Good Answer 10 weeks 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
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Popular Question 3 months ago, created a question with more than 1,000 views. For Assemble short reads based on k-mers
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 Map a protein domain information to a sequence
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Popular Question 4 months ago, created a question with more than 1,000 views. For Map a protein domain information to a sequence
Scholar 4 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Scholar 5 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
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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 6 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Appreciated 6 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 6 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
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
Teacher 8 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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