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RRBSdata
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edgeR, RRBS Library size preparation
RRBSdata
edgeR
methylationArrayAnalysis
10 months ago
Krzysztof
• 0
0
votes
3
replies
389
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annasoudi
• 0
0
votes
11
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1.6k
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Differential methilation analysis - Design matrix not of full rank
DifferentialMethylation
RRBSdata
edgeR
updated 2.0 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Mageiros
• 0
0
votes
1
reply
961
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Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Mageiros
• 0
0
votes
2
replies
872
views
Locating nearest genes in RRBS analysis
hiAnnotator
bsseq
DifferentialMethylation
edgeR
RRBSdata
2.0 years ago • updated 23 months ago
Mageiros
• 0
5 results • Page
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Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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