Showing : biseq • reset
0
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1
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834
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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
votes
0
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933
views
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
votes
1
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1.2k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
4.6 years ago • updated 4.5 years ago akhaira • 0
0
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1
reply
907
views
testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
4.6 years ago akhaira • 0
2
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8
replies
1.3k
views
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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604
views
What values to include for predictedMethNull in BiSeq
Biseq
4.6 years ago akhaira • 0
2
votes
10
replies
1.7k
views
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
replies
755
views
Understanding ColData in BiSeq
BiSeq Coldata
4.7 years ago akhaira • 0
0
votes
1
reply
827
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.7 years ago AishaD • 0
0
votes
1
reply
782
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.9 years ago i.s.castanho • 0
0
votes
0
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911
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq Wald test Beta regression
6.0 years ago mira • 0
0
votes
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
votes
0
replies
1.1k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
6.5 years ago spr ▴ 10
0
votes
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
votes
1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
7.8 years ago l.eijssen • 0
0
votes
3
replies
1.5k
views
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
votes
6
replies
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 ▴ 680
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
vote
2
replies
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 ▴ 680
2
votes
15
replies
3.6k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
9.8 years ago • updated 9.7 years ago mnaymik ▴ 10
0
votes
5
replies
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
replies
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: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
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FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
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Thanks James!
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Answer: Unable to install nloptr
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C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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