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## Progress Report of Bloodies
#### What has changed based on the final proposal
We are using the same datasets as proposed but has eliminated a few samples from the analysis. For example, we remov…
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Hi,
I am interested in finding differentially methylated regions, and I have processed my PE-reads with Bismark.
I wanted to try DMRfinder to identify DMR, but I wanted to ask a question before mo…
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Hello,
I ran a preliminary experiment to see if the all contexts methylation models work in an unusual system. Basically, I amplified the whole genome to remove any marks, then treated samples with…
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RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
http://bioinformatics.oxfordjournals.org/content/30/12/i283.full.pdf+html
Li HD, Menon R, Omenn GS, Guan Y. (2014) The emerging…
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Hi,
I'm a big fan of `bsseq` because it is exactly the data structure I need for a package I maintain (`methylSig`) that tests for differential methylation (at CpGs and over regions).
As of the …
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(Please excuse my amateur approach to this I am relatively new to this viewer!)
I was wondering if anyone could help me out with quantifying DNA Methylation on IGV when you are comparing two file…
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Hey people,
I will also try to put down what I remember of Amrits conversation with us.
- Look at differential network analysis. This can be used to see the differences in networks between the…
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Dear yupenghe,
Why DMR does not need to distinguish +/- strand like DMS ?
Thanks.
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Hi, Ricard @rargelaguet
I am reproducing Extended Data Fig. 6a of the article "Multi-omics profiling of mouse gastrulation at single-cell resolution" . I have currently downloaded Supplementary Table…
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Hi,
I am trying to do DMR on one of our test dataset which has one sample for case and two samples for control. While I was running the diff_methylsig function, I encountered such an error "Error i…