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biseq
•
reset
2
votes
15
replies
3.0k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.1 years ago • updated 9.0 years ago
mnaymik
▴ 10
2
votes
10
replies
1.2k
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
2
votes
8
replies
933
views
Reason for NA in table after beta regression?
biseq
beta regression
3.8 years ago
akhaira
• 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
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
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
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
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
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
0
votes
1
reply
635
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.2 years ago
thomas.koefoed
• 0
0
votes
1
reply
1.1k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.1 years ago
l.eijssen
• 0
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
928
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
1
reply
609
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.1 years ago
i.s.castanho
• 0
0
votes
1
reply
643
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.0 years ago
AishaD
• 0
0
votes
1
reply
729
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
3.8 years ago
akhaira
• 0
0
votes
1
reply
921
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
0
replies
473
views
What values to include for predictedMethNull in BiSeq
Biseq
3.9 years ago
akhaira
• 0
0
votes
0
replies
905
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
5.7 years ago
spr
▴ 10
0
votes
0
replies
750
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
1
vote
0
replies
1.7k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
8.4 years ago
enricoferrero
▴ 660
1
vote
0
replies
576
views
Understanding ColData in BiSeq
BiSeq
Coldata
3.9 years ago
akhaira
• 0
0
votes
0
replies
735
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
5.3 years ago
mira
• 0
23 results • Page
1 of 1
Recent ...
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Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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