User: bioinfouser

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bioinfouser50
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Posts by bioinfouser

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... Dear Rory, one more question. this default library size normalisation in `DiffBind` is done of the raw counts, or? ...
written 11 days ago by bioinfouser50
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Comment: C: Recommendation for packages for cell type deconvolution from bulk RNAseq data?
... Thanks a lot! I am looking for recommendation specifically for brain tissue RNAseq. I will check more extensively then. ...
written 12 days ago by bioinfouser50
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Comment: C: Recommendation for using limma-voom workflow for ChIPseq analysis. Or other tool
... Thank you! I will look into it. My current knowledge tells me, it is a window based tool, rather then "analysing predefined peaks(by macs2, for example)" that I am doing. Could you comment if csaw is more advantageous than defined peak based analysis? ...
written 12 days ago by bioinfouser50
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Recommendation for packages for cell type deconvolution from bulk RNAseq data?
... I was wondering, if you have some recommendation on which R package to use for doing cell-type deconvolution from bulk RNAseq data? I would really appreciate your suggestions! [edit] I am looking for recommendation specifically for brain tissue RNAseq. Any package that you have used in that contex ...
deconvolution rna-seq cell type written 12 days ago by bioinfouser50
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Recommendation for using limma-voom workflow for ChIPseq analysis. Or other tool for capturing global histone mark difference?
... Hello awesome community! I just wanted to know your expert opinion, whether `limma-voom` protocol is suitable for analysing ChIPseq data(with `macs2` peaks and raw read counts generated from `featureCounts`). Does it assume that majority of the expression will not change among groups, just like `DE ...
chip-seq written 16 days ago by bioinfouser50
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Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
... Thank you! I will look into it more! ...
written 16 days ago by bioinfouser50
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Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
... Thank you very much! That's very helpful! ...
written 17 days ago by bioinfouser50
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How to avoid hardcoding in R? How to automatize R scripts?
... Hello, This is not directly related to any particular analysis. I have been doing my own analysis for rna seq data for the last one year, completely learning from here and there. Until now, I am confident and can do my own analysis. I always use Rstudio to write and run the scripts for my data anal ...
R chip-seq r programming rna-seq written 18 days ago by bioinfouser50
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... Dear Rory, Thank you very much for your swift reply! I understand now completely! I will do my analysis accordingly. One last question regarding normalisation, if I use `DESeq2` normalization for ChIPseq analysis, would it equal to `DiffBind` simple normalisation in terms of the results? Also, I ...
written 24 days ago by bioinfouser50
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... I will go through the link. Thanks! ...
written 26 days ago by bioinfouser50

Latest awards to bioinfouser

Popular Question 28 days ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r
Supporter 8 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r
Popular Question 21 months ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r

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