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Biseq
•
reset
0
votes
1
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776
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.8 years ago • updated 2.7 years ago
thomas.koefoed
• 0
0
votes
0
replies
889
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.3 years ago
i.s.castanho
• 0
0
votes
1
reply
1.1k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
4.3 years ago
akhaira
• 0
0
votes
1
reply
856
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
4.4 years ago • updated 4.3 years ago
akhaira
• 0
2
votes
8
replies
1.2k
views
Reason for NA in table after beta regression?
biseq
beta regression
4.4 years ago
akhaira
• 0
0
votes
0
replies
573
views
What values to include for predictedMethNull in BiSeq
Biseq
4.4 years ago
akhaira
• 0
2
votes
10
replies
1.5k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 4.4 years ago by
James W. MacDonald
67k • written 4.4 years ago by
akhaira
• 0
1
vote
0
replies
710
views
Understanding ColData in BiSeq
BiSeq
Coldata
4.4 years ago
akhaira
• 0
0
votes
1
reply
785
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.5 years ago
AishaD
• 0
0
votes
1
reply
746
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.6 years ago
i.s.castanho
• 0
0
votes
0
replies
865
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
5.8 years ago
mira
• 0
0
votes
1
reply
1.1k
views
Biseq installation error
biseq
package installation
r
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
lwh863
• 0
0
votes
0
replies
1.1k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
6.3 years ago
spr
▴ 10
0
votes
1
reply
1.2k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.9 years ago by
Gordon Smyth
51k • written 6.9 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.2k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.6 years ago
l.eijssen
• 0
0
votes
3
replies
1.4k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 7.8 years ago by
Katja Hebestreit
▴ 130 • written 7.8 years ago by
jjalmagro
• 0
0
votes
6
replies
2.1k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 8.8 years ago by
Katja Hebestreit
▴ 130 • written 8.8 years ago by
kms68
• 0
1
vote
0
replies
1.8k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
8.9 years ago
enricoferrero
▴ 660
4
votes
4
replies
2.0k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
Neel Aluru
▴ 460
1
vote
2
replies
2.7k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 9.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.1 years ago by
enricoferrero
▴ 660
2
votes
15
replies
3.4k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.6 years ago • updated 9.5 years ago
mnaymik
▴ 10
0
votes
5
replies
2.2k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.5 years ago
maria.maqueda
• 0
0
votes
3
replies
1.9k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 10.8 years ago by
David Iles
▴ 130 • written 10.8 years ago by
Hans-Ulrich Klein
▴ 330
23 results • Page
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GV Yoshikawa
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Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet
by
Gordon Smyth
51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Adam
• 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Comment: Problem at champ.load
by
icecreamlover
• 0
Hello! Were you able to figure this out? I am running into the same error!
Comment: ChAMP - obtaining beta values using EPICv2 annotation
by
icecreamlover
• 0
Hello, Were you able to fix the error? I used the same document and I am running into the same error. I am curious if you have any feedba…
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