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RRBS
•
reset
4
votes
5
replies
836
views
edgeR for a mixture experiment
edgeR
model-selection
RRBS
mixture-experiment
2.5 years ago
ingerslev
• 0
0
votes
2
replies
658
views
MethylCC for RRBS data of Cord Blood
MethylCC
RRBS
cord blood
3.2 years ago
weichen-cls
• 0
0
votes
0
replies
543
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
3.2 years ago
i.s.castanho
• 0
0
votes
1
reply
446
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
3.5 years ago
i.s.castanho
• 0
5
votes
14
replies
1.7k
views
Odd P-value distribution in edgeR on RRBS data
edgeR
rrbs
updated 4.7 years ago by
Gordon Smyth
48k • written 4.7 years ago by
ingerslev
• 0
0
votes
4
replies
1.8k
views
MethylKit read in issue
methykit
rrbs
updated 5.4 years ago by
Mike Smith
★ 6.1k • written 5.4 years ago by
bekah
▴ 20
0
votes
3
replies
1.3k
views
scalability of edgeR on RRBS methylation data
edgeR
methyation
RRBS
updated 5.7 years ago by
Gordon Smyth
48k • written 5.7 years ago by
osa.zuta
▴ 40
0
votes
1
reply
963
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
6.5 years ago
l.eijssen
• 0
1
vote
4
replies
1.6k
views
Using SVA with RRBS data
sva
RRBS
updated 6.6 years ago by
Jeff Leek
▴ 640 • written 6.6 years ago by
mrodrigues.fernanda
▴ 10
0
votes
3
replies
1.6k
views
SVA package for RRBS - bisulfite methylation data
rrbs
batch effect
methylation
sva
updated 7.0 years ago by
dashbrook1
• 0 • written 8.2 years ago by
GFM
▴ 20
4
votes
2
replies
1.2k
views
Bounded Regression with Limma for RRBS?
limma
rrbs
bsseq
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
nhejazi
• 0
0
votes
5
replies
1.7k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
8.4 years ago
maria.maqueda
• 0
12 results • Page
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Answer: Is SeqSQC compatible with hg38?
by
James W. MacDonald
63k
I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on t…
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of
by
Gregory
• 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus
by
Rory Stark
★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles)
by
Rory Stark
★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles)
by
Dorien
▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Votes
Answer: How do I merge a list of GRanges?
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
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