Showing : BiSeq • reset
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831
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Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.0 years ago thomas.koefoed • 0
0
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0
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931
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.5 years ago i.s.castanho • 0
0
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1
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1.2k
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How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
4.5 years ago akhaira • 0
0
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1
reply
905
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testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
4.6 years ago akhaira • 0
2
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8
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1.3k
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Reason for NA in table after beta regression?
biseq beta regression
4.6 years ago akhaira • 0
0
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0
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603
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What values to include for predictedMethNull in BiSeq
Biseq
4.6 years ago akhaira • 0
2
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10
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1.7k
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How do you use the readBismark command in BiSeq properly?
BiSeq DMR
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
1
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0
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754
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Understanding ColData in BiSeq
BiSeq Coldata
4.7 years ago akhaira • 0
0
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1
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823
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.7 years ago AishaD • 0
0
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1
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777
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BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.8 years ago i.s.castanho • 0
0
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0
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910
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq Wald test Beta regression
6.0 years ago mira • 0
0
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1
reply
1.2k
views
Biseq installation error
biseq package installation r
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
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0
replies
1.1k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
6.5 years ago spr ▴ 10
0
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1
reply
1.3k
views
Problem in working with BiSeq - BSraw
dna methylation biseq
updated 7.1 years ago by 52k • written 7.1 years ago by • 0
0
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1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
7.8 years ago l.eijssen • 0
0
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3
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1.5k
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BiSeq. Model beta regression on resampled data.
biseq methylation dmr analysis
updated 8.1 years ago by ▴ 130 • written 8.1 years ago by • 0
0
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6
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2.1k
views
BiSeq trimClusters error
biseq error trimClusters
updated 9.0 years ago by ▴ 130 • written 9.0 years ago by • 0
1
vote
0
replies
1.9k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
9.1 years ago enricoferrero ▴ 660
4
votes
4
replies
2.1k
views
Unable to read data using readBismark in BiSeq
BiSeq readBismark
updated 9.2 years ago by 67k • written 9.2 years ago by ▴ 460
1
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2
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2.8k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 9.3 years ago by ★ 6.5k • written 9.3 years ago by ▴ 660
2
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15
replies
3.5k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
9.8 years ago • updated 9.7 years ago mnaymik ▴ 10
0
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5
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2.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.8 years ago • updated 9.7 years ago maria.maqueda • 0
0
votes
3
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1.9k
views
BiSeq - readBismark error
BiSeq BiSeq
updated 11.0 years ago by ▴ 130 • written 11.0 years ago by ▴ 330
23 results • Page 1 of 1
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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k
Thanks @fep29! ^^
Votes
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
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