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BiSeq
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0
votes
1
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629
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.2 years ago
thomas.koefoed
• 0
0
votes
0
replies
746
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
0
votes
1
reply
917
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
1
reply
725
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
3.8 years ago
akhaira
• 0
2
votes
8
replies
922
views
Reason for NA in table after beta regression?
biseq
beta regression
3.8 years ago
akhaira
• 0
0
votes
0
replies
471
views
What values to include for predictedMethNull in BiSeq
Biseq
3.8 years ago
akhaira
• 0
2
votes
10
replies
1.1k
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
1
vote
0
replies
572
views
Understanding ColData in BiSeq
BiSeq
Coldata
3.9 years ago
akhaira
• 0
0
votes
1
reply
636
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
604
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
4.1 years ago
i.s.castanho
• 0
0
votes
0
replies
730
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
5.2 years ago
mira
• 0
0
votes
1
reply
922
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
0
replies
901
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
5.7 years ago
spr
▴ 10
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
1.1k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
7.1 years ago
l.eijssen
• 0
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
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
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
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
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
2
votes
15
replies
3.0k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.0 years ago • updated 8.9 years ago
mnaymik
▴ 10
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
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
23 results • Page
1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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