Showing : Biseq • reset
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
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
0
votes
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
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
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
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
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
910
views
Biseq installation error
biseq package installation r
updated 5.3 years ago by 25k • written 5.3 years ago by • 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
0
votes
0
replies
891
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
5.7 years ago spr ▴ 10
0
votes
0
replies
740
views
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
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
599
views
BiSeq - betaResults output only contains chr1 and chr2
biseq betaRegression RRBS Methylation
4.1 years ago i.s.castanho • 0
0
votes
1
reply
623
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
3.9 years ago AishaD • 0
1
vote
0
replies
565
views
Understanding ColData in BiSeq
BiSeq Coldata
3.9 years ago akhaira • 0
0
votes
1
reply
622
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
2.2 years ago thomas.koefoed • 0
0
votes
0
replies
465
views
What values to include for predictedMethNull in BiSeq
Biseq
3.8 years ago akhaira • 0
2
votes
8
replies
909
views
Reason for NA in table after beta regression?
biseq beta regression
3.8 years ago akhaira • 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
0
votes
1
reply
721
views
testClusters and trimClusters error in BiSeq
BiSeq testClusters error dmr
3.8 years ago akhaira • 0
0
votes
1
reply
1.1k
views
BiSeq - modelling options betaRegression
biseq RRBS betaregression
7.0 years ago l.eijssen • 0
0
votes
1
reply
910
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
3.8 years ago akhaira • 0
23 results • Page 1 of 1
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Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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