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rrbs
•
reset
4
votes
5
replies
1.3k
views
edgeR for a mixture experiment
edgeR
model-selection
RRBS
mixture-experiment
3.8 years ago
ingerslev
• 0
0
votes
2
replies
1.1k
views
MethylCC for RRBS data of Cord Blood
MethylCC
RRBS
cord blood
4.5 years ago
weichen-cls
• 0
0
votes
0
replies
934
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.5 years ago
i.s.castanho
• 0
0
votes
1
reply
783
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.9 years ago
i.s.castanho
• 0
5
votes
14
replies
2.5k
views
Odd P-value distribution in edgeR on RRBS data
edgeR
rrbs
updated 6.1 years ago by
Gordon Smyth
52k • written 6.1 years ago by
ingerslev
• 0
0
votes
4
replies
2.8k
views
MethylKit read in issue
methykit
rrbs
updated 6.7 years ago by
Mike Smith
★ 6.6k • written 6.7 years ago by
bekah
▴ 40
0
votes
3
replies
1.8k
views
scalability of edgeR on RRBS methylation data
edgeR
methyation
RRBS
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 years ago by
osa.zuta
▴ 40
0
votes
1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.8 years ago
l.eijssen
• 0
1
vote
4
replies
2.2k
views
Using SVA with RRBS data
sva
RRBS
updated 7.9 years ago by
Jeff Leek
▴ 650 • written 7.9 years ago by
mrodrigues.fernanda
▴ 10
0
votes
3
replies
2.0k
views
SVA package for RRBS - bisulfite methylation data
rrbs
batch effect
methylation
sva
updated 8.3 years ago by
dashbrook1
• 0 • written 9.5 years ago by
GFM
▴ 20
4
votes
2
replies
1.7k
views
Bounded Regression with Limma for RRBS?
limma
rrbs
bsseq
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
nhejazi
• 0
0
votes
5
replies
2.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.8 years ago • updated 9.7 years ago
maria.maqueda
• 0
12 results • Page
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Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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