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Biseq
•
reset
2
votes
15
replies
1.9k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
7.1 years ago • updated 7.0 years ago
mnaymik
▴ 10
0
votes
6
replies
1.3k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 6.3 years ago by
Katja Hebestreit
▴ 130 • written 6.4 years ago by
kms68
• 0
0
votes
5
replies
1.4k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
7.1 years ago
maria.maqueda
• 0
0
votes
3
replies
1.3k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 8.3 years ago by
David Iles
▴ 130 • written 8.3 years ago by
Hans-Ulrich Klein
▴ 330
1
vote
2
replies
1.8k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 6.6 years ago by
Kasper Daniel Hansen
6.5k • written 6.6 years ago by
enricoferrero
▴ 610
4
votes
4
replies
1.2k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 6.6 years ago by
James W. MacDonald
60k • written 6.6 years ago by
Neel Aluru
▴ 460
0
votes
3
replies
812
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 5.4 years ago by
Katja Hebestreit
▴ 130 • written 5.4 years ago by
jjalmagro
• 0
0
votes
1
reply
589
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 4.4 years ago by
Gordon Smyth
45k • written 4.4 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
371
views
Biseq installation error
biseq
package installation
r
updated 3.4 years ago by
Martin Morgan
25k • written 3.4 years ago by
lwh863
• 0
2
votes
10
replies
312
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 23 months ago by
James W. MacDonald
60k • written 23 months ago by
akhaira
• 0
0
votes
0
replies
510
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
3.8 years ago
spr
▴ 10
0
votes
0
replies
244
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
22 months ago
i.s.castanho
• 0
0
votes
0
replies
371
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
3.3 years ago
mira
• 0
0
votes
1
reply
194
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
2.2 years ago
i.s.castanho
• 0
0
votes
1
reply
214
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
2.0 years ago
AishaD
• 0
1
vote
0
replies
253
views
Understanding ColData in BiSeq
BiSeq
Coldata
24 months ago
akhaira
• 0
0
votes
1
reply
134
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3 months ago
thomas.koefoed
• 0
0
votes
0
replies
167
views
What values to include for predictedMethNull in BiSeq
Biseq
23 months ago
akhaira
• 0
2
votes
8
replies
344
views
Reason for NA in table after beta regression?
biseq
beta regression
23 months ago
akhaira
• 0
1
vote
0
replies
1.2k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
6.5 years ago
enricoferrero
▴ 610
0
votes
1
reply
269
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
23 months ago • updated 22 months ago
akhaira
• 0
0
votes
1
reply
675
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
5.1 years ago
l.eijssen
• 0
0
votes
1
reply
321
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
22 months ago
akhaira
• 0
23 results • Page
1 of 1
Recent ...
Replies
Comment: Subsetting operation on CompressedGRangesList object 'x' produces a result tha
by
Jiping Wang
▴ 70
that's terrific. thanks. thanks for your comment on `pcoverageByTranscript` function as well. yes, we understand it's for transcript. that…
Answer: Help with constructing design matrix for edgeR/limma
by
Gordon Smyth
45k
If the infertile subpopulations have different expression profiles then you need ``` design <- model.matrix(~Pathology) ``` and not includ…
Comment: edgeR : results from goana and kegga functions show opposite sig. p-value
by
sharvari gujja
▴ 30
Thank you so much!
Comment: Subsetting operation on CompressedGRangesList object 'x' produces a result tha
by
Hervé Pagès
15k
Hi Jiping, Sorry for the slow response and thanks for providing those details. They allowed me to reproduce the problem and to come up wit…
Answer: Trouble with detecting AS events using ASpediaFI
by
rbqlsrbqls56
• 0
Assuming you downloaded "Homo_sapiens.GRCh38.104.gtf" from the Ensembl website, the gene model contains reference chromosomes (chr1-22, X, …
Votes
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
Answer: paired analysis : return data matrix with indvidual/subject effects eliminated.
DESeq2: likelihood ratio test interpretation, multifactor
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
Answer: GDCprepare of RNAseq counts produces error
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