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biseq
•
reset
2
votes
15
replies
3.3k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.4 years ago
mnaymik
▴ 10
0
votes
6
replies
2.0k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 8.6 years ago by
Katja Hebestreit
▴ 130 • written 8.7 years ago by
kms68
• 0
0
votes
5
replies
2.2k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.4 years ago
maria.maqueda
• 0
0
votes
3
replies
1.8k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 10.6 years ago by
David Iles
▴ 130 • written 10.6 years ago by
Hans-Ulrich Klein
▴ 330
1
vote
2
replies
2.7k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 8.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.9 years ago by
enricoferrero
▴ 660
4
votes
4
replies
2.0k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 8.9 years ago by
James W. MacDonald
67k • written 8.9 years ago by
Neel Aluru
▴ 460
0
votes
3
replies
1.4k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 7.7 years ago by
Katja Hebestreit
▴ 130 • written 7.7 years ago by
jjalmagro
• 0
0
votes
1
reply
1.2k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.7 years ago by
Gordon Smyth
51k • written 6.7 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.1k
views
Biseq installation error
biseq
package installation
r
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
lwh863
• 0
2
votes
10
replies
1.4k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 4.3 years ago by
James W. MacDonald
67k • written 4.3 years ago by
akhaira
• 0
0
votes
0
replies
1.0k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
6.1 years ago
spr
▴ 10
0
votes
0
replies
854
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.2 years ago
i.s.castanho
• 0
0
votes
0
replies
841
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
5.6 years ago
mira
• 0
0
votes
1
reply
714
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.5 years ago
i.s.castanho
• 0
0
votes
1
reply
735
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.4 years ago
AishaD
• 0
1
vote
0
replies
680
views
Understanding ColData in BiSeq
BiSeq
Coldata
4.3 years ago
akhaira
• 0
0
votes
1
reply
739
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.6 years ago
thomas.koefoed
• 0
0
votes
0
replies
553
views
What values to include for predictedMethNull in BiSeq
Biseq
4.2 years ago
akhaira
• 0
2
votes
8
replies
1.1k
views
Reason for NA in table after beta regression?
biseq
beta regression
4.2 years ago
akhaira
• 0
1
vote
0
replies
1.8k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
8.8 years ago
enricoferrero
▴ 660
0
votes
1
reply
829
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
4.2 years ago
akhaira
• 0
0
votes
1
reply
1.2k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.5 years ago
l.eijssen
• 0
0
votes
1
reply
1.1k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
4.2 years ago
akhaira
• 0
23 results • Page
1 of 1
Recent ...
Replies
Comment: Question on performing ANOVA-like analysis using limma
by
Gordon Smyth
51k
What does `sampleid` represent? If you use duplicateCorrelation(), then the blocking factor should be subject, it isn't clear from your que…
Answer: Question on performing ANOVA-like analysis using limma
by
Gordon Smyth
51k
In time course experiments such as this, it is essential to account for baseline variability between subjects, so the second analysis given…
Comment: AffylmGUI does not start wit R 4.4.1
by
Gordon Smyth
51k
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Answer: rtracklayer accessing UCSC data table not working
by
James W. MacDonald
67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
Answer: For feline genome
by
James W. MacDonald
67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
Votes
Comment: AffylmGUI does not start wit R 4.4.1
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
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