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BiSeq
•
reset
0
votes
1
reply
627
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.2 years ago
thomas.koefoed
• 0
0
votes
0
replies
743
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
3.8 years ago
i.s.castanho
• 0
0
votes
1
reply
913
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
3.8 years ago
akhaira
• 0
0
votes
1
reply
722
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
3.8 years ago
akhaira
• 0
2
votes
8
replies
916
views
Reason for NA in table after beta regression?
biseq
beta regression
3.8 years ago
akhaira
• 0
0
votes
0
replies
467
views
What values to include for predictedMethNull in BiSeq
Biseq
3.8 years ago
akhaira
• 0
2
votes
10
replies
1.1k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
akhaira
• 0
1
vote
0
replies
569
views
Understanding ColData in BiSeq
BiSeq
Coldata
3.9 years ago
akhaira
• 0
0
votes
1
reply
629
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
3.9 years ago
AishaD
• 0
0
votes
1
reply
601
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.1 years ago
i.s.castanho
• 0
0
votes
0
replies
727
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
5.2 years ago
mira
• 0
0
votes
1
reply
914
views
Biseq installation error
biseq
package installation
r
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
lwh863
• 0
0
votes
0
replies
895
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
5.7 years ago
spr
▴ 10
0
votes
1
reply
1.1k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.1k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.1 years ago
l.eijssen
• 0
0
votes
3
replies
1.3k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 7.3 years ago by
Katja Hebestreit
▴ 130 • written 7.3 years ago by
jjalmagro
• 0
0
votes
6
replies
1.9k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 8.2 years ago by
Katja Hebestreit
▴ 130 • written 8.3 years ago by
kms68
• 0
1
vote
0
replies
1.6k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
8.4 years ago
enricoferrero
▴ 660
4
votes
4
replies
1.9k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 8.5 years ago by
James W. MacDonald
65k • written 8.5 years ago by
Neel Aluru
▴ 460
1
vote
2
replies
2.5k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 8.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.5 years ago by
enricoferrero
▴ 660
2
votes
15
replies
3.0k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.0 years ago • updated 8.9 years ago
mnaymik
▴ 10
0
votes
5
replies
2.0k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.0 years ago
maria.maqueda
• 0
0
votes
3
replies
1.7k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 10.2 years ago by
David Iles
▴ 130 • written 10.2 years ago by
Hans-Ulrich Klein
▴ 330
23 results • Page
1 of 1
Recent ...
Replies
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates
by
hortense96
• 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp
by
Basti
▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none
by
WardDeb
• 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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