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biseq
•
reset
0
votes
1
reply
850
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.0 years ago
thomas.koefoed
• 0
0
votes
0
replies
940
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
4.6 years ago
i.s.castanho
• 0
0
votes
1
reply
1.2k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
4.6 years ago
akhaira
• 0
0
votes
1
reply
914
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
4.6 years ago
akhaira
• 0
2
votes
8
replies
1.3k
views
Reason for NA in table after beta regression?
biseq
beta regression
4.6 years ago
akhaira
• 0
0
votes
0
replies
609
views
What values to include for predictedMethNull in BiSeq
Biseq
4.6 years ago
akhaira
• 0
2
votes
10
replies
1.7k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 4.7 years ago by
James W. MacDonald
68k • written 4.7 years ago by
akhaira
• 0
1
vote
0
replies
766
views
Understanding ColData in BiSeq
BiSeq
Coldata
4.7 years ago
akhaira
• 0
0
votes
1
reply
842
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
4.8 years ago
AishaD
• 0
0
votes
1
reply
802
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.9 years ago
i.s.castanho
• 0
0
votes
0
replies
919
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
6.0 years ago
mira
• 0
0
votes
1
reply
1.2k
views
Biseq installation error
biseq
package installation
r
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
lwh863
• 0
0
votes
0
replies
1.1k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
6.5 years ago
spr
▴ 10
0
votes
1
reply
1.3k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.9 years ago
l.eijssen
• 0
0
votes
3
replies
1.5k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 8.1 years ago by
Katja Hebestreit
▴ 130 • written 8.1 years ago by
jjalmagro
• 0
0
votes
6
replies
2.1k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 9.0 years ago by
Katja Hebestreit
▴ 130 • written 9.1 years ago by
kms68
• 0
1
vote
0
replies
1.9k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
9.2 years ago
enricoferrero
▴ 680
4
votes
4
replies
2.1k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 9.3 years ago by
James W. MacDonald
68k • written 9.3 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 9.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.3 years ago by
enricoferrero
▴ 680
2
votes
15
replies
3.6k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.8 years ago • updated 9.7 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
9.8 years ago
maria.maqueda
• 0
0
votes
3
replies
1.9k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 11.0 years ago by
David Iles
▴ 130 • written 11.0 years ago by
Hans-Ulrich Klein
▴ 330
23 results • Page
1 of 1
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Comment: For some reason I can't update BiocManager to 3.20
by
shepherl
4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.6k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Comment: MEDIPS - error using MEDIPS.CpGenrich
by
sg
• 0
I have the same error when I use 22 chrs with the paramenters chr.select: Error in h(simpleError(msg, call)) : error in evaluating the …
Comment: Overcoming confounding in batch effect correction
by
mimi
• 0
https://www.bioconductor.org/packages/release/BiocViews.html#___BiologicalQuestion
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Votes
Overcoming confounding in batch effect correction
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
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