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BiSeq
•
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0
votes
1
reply
799
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.8 years ago
thomas.koefoed
• 0
0
votes
0
replies
907
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.4 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
4.4 years ago
akhaira
• 0
0
votes
1
reply
878
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
4.4 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
587
views
What values to include for predictedMethNull in BiSeq
Biseq
4.5 years ago
akhaira
• 0
2
votes
10
replies
1.6k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
akhaira
• 0
1
vote
0
replies
722
views
Understanding ColData in BiSeq
BiSeq
Coldata
4.5 years ago
akhaira
• 0
0
votes
1
reply
805
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.6 years ago
AishaD
• 0
0
votes
1
reply
759
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.7 years ago
i.s.castanho
• 0
0
votes
0
replies
887
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
5.9 years ago
mira
• 0
0
votes
1
reply
1.1k
views
Biseq installation error
biseq
package installation
r
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 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
1.3k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.7 years ago
l.eijssen
• 0
0
votes
3
replies
1.5k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 7.9 years ago by
Katja Hebestreit
▴ 130 • written 7.9 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 8.9 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
9.0 years ago
enricoferrero
▴ 660
4
votes
4
replies
2.1k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 9.1 years ago by
James W. MacDonald
67k • written 9.1 years ago by
Neel Aluru
▴ 460
1
vote
2
replies
2.8k
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
3.5k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.7 years ago • updated 9.6 years ago
mnaymik
▴ 10
0
votes
5
replies
2.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.6 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
1 of 1
Recent ...
Replies
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
ATpoint
★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
swbarnes2
★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
Comment: RSubread output significantly different from bash Subread output
by
Aimee
• 0
Hi Gordon, Thank you so much for this response. I went back and checked, and you are absolutely correct that it was shown in the settings b…
Answer: Can we get beta values with DMRcate package
by
James W. MacDonald
67k
If you get an error that says ``` Error in getCollapsedBetas(myAnnotation) : could not find function "getCollapsedBetas" ``` It …
Comment: What type of counts data to import for performing Isoform analysis in edgeR
by
ATpoint
★ 4.6k
I think this already happened, see https://github.com/nf-core/rnasplice/issues/162
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
Awards
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Teacher
to
Gordon Smyth
52k
Scholar
to
Aaron Lun
★ 28k
Teacher
to
Michael Love
43k
Popular Question
to
Dario Strbenac
★ 1.5k
Scholar
to
ATpoint
★ 4.6k
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