Showing : Biseq • reset
0
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895
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Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.2 years ago thomas.koefoed • 0
0
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0
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974
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Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.7 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
4.7 years ago akhaira • 0
0
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1
reply
940
views
testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
4.8 years ago • updated 4.7 years ago akhaira • 0
2
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8
replies
1.4k
views
Reason for NA in table after beta regression?
biseq beta regression
4.8 years ago akhaira • 0
0
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0
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642
views
What values to include for predictedMethNull in BiSeq
Biseq
4.8 years ago akhaira • 0
2
votes
10
replies
1.8k
views
How do you use the readBismark command in BiSeq properly?
BiSeq DMR
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
1
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0
replies
806
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Understanding ColData in BiSeq
BiSeq Coldata
4.9 years ago akhaira • 0
0
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1
reply
888
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
4.9 years ago AishaD • 0
0
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1
reply
833
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
5.0 years ago i.s.castanho • 0
0
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0
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964
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq Wald test Beta regression
6.2 years ago mira • 0
0
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1
reply
1.2k
views
Biseq installation error
biseq package installation r
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
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0
replies
1.1k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
6.7 years ago spr ▴ 10
0
votes
1
reply
1.3k
views
Problem in working with BiSeq - BSraw
dna methylation biseq
updated 7.3 years ago by 52k • written 7.3 years ago by • 0
0
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1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
8.0 years ago l.eijssen • 0
0
votes
3
replies
1.5k
views
BiSeq. Model beta regression on resampled data.
biseq methylation dmr analysis
updated 8.3 years ago by ▴ 130 • written 8.3 years ago by • 0
0
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6
replies
2.2k
views
BiSeq trimClusters error
biseq error trimClusters
updated 9.2 years ago by ▴ 130 • written 9.2 years ago by • 0
1
vote
0
replies
1.9k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
9.3 years ago enricoferrero ▴ 680
4
votes
4
replies
2.2k
views
Unable to read data using readBismark in BiSeq
BiSeq readBismark
updated 9.4 years ago by 68k • written 9.4 years ago by ▴ 460
1
vote
2
replies
2.9k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 9.5 years ago by ★ 6.5k • written 9.5 years ago by ▴ 680
2
votes
15
replies
3.7k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
10.0 years ago • updated 9.9 years ago mnaymik ▴ 10
0
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5
replies
2.4k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.9 years ago maria.maqueda • 0
0
votes
3
replies
2.0k
views
BiSeq - readBismark error
BiSeq BiSeq
updated 11.2 years ago by ▴ 130 • written 11.2 years ago by ▴ 330
23 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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