Showing : biseq • reset
0
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1
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625
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Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.2 years ago thomas.koefoed • 0
0
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0
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741
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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
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1
reply
721
views
testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
3.8 years ago akhaira • 0
2
votes
8
replies
910
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Reason for NA in table after beta regression?
biseq beta regression
3.8 years ago akhaira • 0
0
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0
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466
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 65k • written 3.8 years ago by • 0
1
vote
0
replies
566
views
Understanding ColData in BiSeq
BiSeq Coldata
3.9 years ago akhaira • 0
0
votes
1
reply
626
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
600
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
911
views
Biseq installation error
biseq package installation r
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
0
votes
0
replies
892
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 50k • written 6.3 years ago by • 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 ▴ 130 • written 7.3 years ago by • 0
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
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 65k • written 8.5 years ago by ▴ 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 ★ 6.5k • written 8.5 years ago by ▴ 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
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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 ▴ 130 • written 10.2 years ago by ▴ 330
23 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
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…
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
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
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