Showing : BiSeq • reset
2
votes
15
replies
3.8k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
10.0 years ago • updated 9.9 years ago mnaymik ▴ 10
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
0
votes
5
replies
2.4k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
10.0 years ago maria.maqueda • 0
0
votes
6
replies
2.2k
views
BiSeq trimClusters error
biseq error trimClusters
updated 9.2 years ago by ▴ 130 • written 9.3 years ago by • 0
4
votes
4
replies
2.2k
views
Unable to read data using readBismark in BiSeq
BiSeq readBismark
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 460
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
1
vote
0
replies
1.9k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
9.4 years ago enricoferrero ▴ 680
2
votes
10
replies
1.8k
views
How do you use the readBismark command in BiSeq properly?
BiSeq DMR
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
votes
3
replies
1.6k
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
2
votes
8
replies
1.4k
views
Reason for NA in table after beta regression?
biseq beta regression
4.8 years ago akhaira • 0
0
votes
1
reply
1.3k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
8.1 years ago l.eijssen • 0
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
votes
1
reply
1.3k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
4.8 years ago akhaira • 0
0
votes
1
reply
1.2k
views
Biseq installation error
biseq package installation r
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
0
votes
0
replies
1.2k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
6.7 years ago spr ▴ 10
0
votes
0
replies
986
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq Methylation DMP DMR RRBS
4.8 years ago i.s.castanho • 0
0
votes
0
replies
975
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq Wald test Beta regression
6.2 years ago mira • 0
0
votes
1
reply
948
views
testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
4.8 years ago akhaira • 0
0
votes
1
reply
906
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.2 years ago thomas.koefoed • 0
0
votes
1
reply
903
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
5.0 years ago AishaD • 0
0
votes
1
reply
844
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
5.1 years ago i.s.castanho • 0
1
vote
0
replies
817
views
Understanding ColData in BiSeq
BiSeq Coldata
4.9 years ago akhaira • 0
0
votes
0
replies
651
views
What values to include for predictedMethNull in BiSeq
Biseq
4.8 years ago akhaira • 0
23 results • Page 1 of 1
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Comment: DiffBind; Error: No sites have activity greater than filter value by etiennedanis • 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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