User: santos.migueldm

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Posts by santos.migueldm

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Comment: C: Is it possible to use DESeq2 likelihood ratio test for time-course analysis to a
... Dear Michael, Thanks for your reply. According to the paper where DANPOS was described https://www.ncbi.nlm.nih.gov/pubmed/23193179: "nucleosome occupancy is calculated as the counts of adjusted reads covering each base pair in the genome". Adjusted because the read size is adjusted to half of ...
written 5 months ago by santos.migueldm0
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Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
... Hi all, I have analysed some RNA-Seq data using the DESeq2 protocol for analysis of time course experiments between two conditions (http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments). Now I have collected samples for MNa ...
timecourse deseq2 mnase-seq written 5 months ago by santos.migueldm0 • updated 5 months ago by Michael Love25k
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Comment: C: [DESeq2] time series strain-specific differences over time
... Hi Michael, I am analyzing RNA-Seq data from a time-course of a mutant strain and would like to ask you something related to this reply.  Following what is described in the time-course vignette:  - In order to calculate the fold change for mut vs wt at an individual time-point shouldn't we use th ...
written 13 months ago by santos.migueldm0
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Comment: C: What's the criteria used by DESeq2 to calculate log2 fold changes in time-course
... Thanks Gavin! That was truly helpful! ...
written 23 months ago by santos.migueldm0
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What's the criteria used by DESeq2 to calculate log2 fold changes in time-course experiments?
... Hi all, I was following the protocol for analysis of Time course experiments using DESeq2 (http://www.bioconductor.org/help/workflows/rnaseqGene/#time-course-experiments) and came up with a doubt regarding the criteria used to calculate the fold-changes and padj.  In this example the fission data ...
timecourse deseq2 written 23 months ago by santos.migueldm0 • updated 23 months ago by Gavin Kelly560

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