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Biseq
•
reset
0
votes
1
reply
625
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
740
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
3.7 years ago
i.s.castanho
• 0
0
votes
1
reply
911
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
721
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
3.8 years ago
akhaira
• 0
2
votes
8
replies
909
views
Reason for NA in table after beta regression?
biseq
beta regression
3.8 years ago
akhaira
• 0
0
votes
0
replies
465
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 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
akhaira
• 0
1
vote
0
replies
565
views
Understanding ColData in BiSeq
BiSeq
Coldata
3.9 years ago
akhaira
• 0
0
votes
1
reply
623
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
3.9 years ago
AishaD
• 0
0
votes
1
reply
599
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
724
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
910
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
891
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
7.0 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
1.6k
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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Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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★ 3.2k
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shepherl
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Gordon Smyth
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