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My motivation for this issue comes from the following basic problem that I encounter every day. A scientist collects data for a given question in a given subject area and wants to be able to apply the…
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Hi, I'm using a conda env with python 2.7 and when I enter "R --version" it lists the OS version 4.3. Within the py2_7 conda env, I see that the lowest R pkg available is now 3.3.1 (i.e, via typing "c…
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@rbalshaw @farnushfarhadi
the last commit: 7ce221a00db3b079f614041d2bf61afa89c415df
the link to the proposal: https://github.com/STAT540-UBC/team_Methylation-Badassays/blob/master/project_proposal.…
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Hi,
I am analyzing methylation data- finding differentially methylated sites/regions, and I wanted to inquire about suggestions whether my input is good or if I should preprocess with better softwa…
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* **PTHR ID & PTN node:**
GO:0009063 | amino acid catabolic process | IBA with PTN000480319 , locus:2176446 , P38117
* **Sequences with problematic annotation (ID + gene/protein name):**
…
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Hi Wanding,
Thank you for the extensive and useful package!
I have been trying to extract a group of probes specific to a contract variable using the DML() function followed by summaryExtractTest(…
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Sam Bogan Review of “DNA Methylation Analyses” by Steven Roberts, Sam White, and Yaamini Venkataraman
link: https://d.pr/f/332Q5v
Original text is in blue. Suggested text is in red.
General Feedb…
sr320 updated
2 months ago
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Sorry, I didn't see anything about m6A methylation modification of mRNA. I have fastq files that contain the 'MM' and 'ML' tag, and I would like to know how I should use this software for DRS methylat…
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Hi, Illumina discontinued the earlier version of the EPIC array. Can you suggest a way to use RnBeads with EPIC v2.0 data?
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Hi,
I'm looking to some differential methylation analysis on EPIC v2 data. As I understand it, after limma differential analysis, I can collapse the probes into various regions with DMRcate. Howeve…