Showing : biseq • reset
2
votes
15
replies
3.0k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
9.1 years ago • updated 9.0 years ago mnaymik ▴ 10
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 ★ 6.5k • written 8.5 years ago by ▴ 660
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
4
votes
4
replies
1.9k
views
Unable to read data using readBismark in BiSeq
BiSeq readBismark
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 460
0
votes
6
replies
1.9k
views
BiSeq trimClusters error
biseq error trimClusters
updated 8.2 years ago by ▴ 130 • written 8.3 years ago by • 0
0
votes
3
replies
1.7k
views
BiSeq - readBismark error
BiSeq BiSeq
updated 10.2 years ago by ▴ 130 • written 10.2 years ago by ▴ 330
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
0
votes
3
replies
1.3k
views
BiSeq. Model beta regression on resampled data.
biseq methylation dmr analysis
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by • 0
2
votes
10
replies
1.2k
views
How do you use the readBismark command in BiSeq properly?
BiSeq DMR
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
1
reply
1.1k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
7.1 years ago l.eijssen • 0
0
votes
1
reply
1.1k
views
Problem in working with BiSeq - BSraw
dna methylation biseq
updated 6.3 years ago by 50k • written 6.3 years ago by • 0
2
votes
8
replies
933
views
Reason for NA in table after beta regression?
biseq beta regression
3.8 years ago akhaira • 0
0
votes
1
reply
928
views
Biseq installation error
biseq package installation r
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
0
votes
1
reply
921
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
0
replies
905
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
5.7 years ago spr ▴ 10
0
votes
0
replies
750
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
0
replies
735
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq Wald test Beta regression
5.3 years ago mira • 0
0
votes
1
reply
729
views
testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
3.8 years ago akhaira • 0
0
votes
1
reply
643
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
635
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.2 years ago thomas.koefoed • 0
0
votes
1
reply
609
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.1 years ago i.s.castanho • 0
1
vote
0
replies
576
views
Understanding ColData in BiSeq
BiSeq Coldata
3.9 years ago akhaira • 0
0
votes
0
replies
473
views
What values to include for predictedMethNull in BiSeq
Biseq
3.9 years ago akhaira • 0
23 results • Page 1 of 1
Recent ...
Replies
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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