Showing : bsseq • reset
4
votes
9
replies
1.8k
views
Memory errors using read.bismark?
dmrseq bsseq
21 months ago • updated 20 months ago Juan Higareda • 0
0
votes
1
reply
992
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 21 months ago by 68k • written 21 months ago by • 0
6
votes
5
replies
2.3k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 2.4 years ago by ▴ 760 • written 2.5 years ago by ▴ 30
1
vote
3
replies
3.2k
views
read.bismark() ->Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
methylSig bsseq
updated 3.4 years ago by ▴ 760 • written 3.4 years ago by • 0
0
votes
2
replies
1.6k
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
3.7 years ago • updated 3.6 years ago Mageiros • 0
0
votes
1
reply
2.6k
views
Gene level methylation values
methylation methylKit bsseq
updated 4.3 years ago by ▴ 10 • written 4.5 years ago by ▴ 80
0
votes
0
replies
1.2k
views
DSS smoothing RRBS and strand collapse
DSS BSSeq
5.8 years ago stephanie.rialle • 0
0
votes
1
reply
1.2k
views
Varying results from DSS when specifying different BSobj
DSS DSS-single bsseq
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
votes
3
replies
1.8k
views
Determination of Hypo- or Hyper- methylation
dmrseq bsseq
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
1
vote
2
replies
1.5k
views
Request to remove requirement for gr to have widths 1 in BSseq constructor
bsseq r package
updated 7.7 years ago by • 0 • written 7.7 years ago by ▴ 140
7
votes
5
replies
2.7k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 7.7 years ago by ▴ 140
0
votes
6
replies
2.6k
views
BSmooth 'names' attribute must be the same length as the vector
bsseq bsmooth
8.2 years ago ravi.tharakan • 0
1
vote
6
replies
2.5k
views
Unusually long running times for getMeth function since latest release
bsseq delayedarray
updated 8.5 years ago by ▴ 760 • written 8.6 years ago by ★ 1.9k
2
votes
3
replies
2.4k
views
bsseq combineList: how to get an HDF5Array-backed object as return value?
bsseq
updated 8.6 years ago by ▴ 760 • written 8.6 years ago by ▴ 20
0
votes
4
replies
2.5k
views
Error while smoothing BS-seq data with bsseq
bsseq
updated 8.7 years ago by • 0 • written 10.3 years ago by • 0
0
votes
6
replies
2.8k
views
BSmooth error during the smoothing step for a subset of files
bsseq bsmooth
updated 8.8 years ago by ▴ 760 • written 8.8 years ago by • 0
0
votes
1
reply
1.7k
views
warning message with BSseq function
bsseq
updated 8.9 years ago by ★ 6.5k • written 8.9 years ago by • 0
1
vote
3
replies
1.9k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq bsmooth
9.0 years ago zuupcat • 0
0
votes
0
replies
1.4k
views
A few questions about BSseq package
bsseq
9.1 years ago Stephen • 0
0
votes
0
replies
1.4k
views
Does bsseq package work with technical replicates?
bsseq WGBS
9.1 years ago Welliton de Souza ▴ 70
4
votes
2
replies
2.0k
views
Bounded Regression with Limma for RRBS?
limma rrbs bsseq
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
0
votes
3
replies
2.4k
views
Is there any way to set bsseq object as 'smoothed'?
bsseq bisulfite
9.7 years ago biohack92 • 0
1
vote
3
replies
2.4k
views
bsseq BSmooth error
bsseq
9.8 years ago enricoferrero ▴ 680
7
votes
11
replies
5.0k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq dmr ttest pvalue
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 680
1
vote
0
replies
2.1k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
10.1 years ago enricoferrero ▴ 680
6
votes
14
replies
6.8k
views
How to correctly import Bismark coverage files into bsseq?
bsseq bismark methylation
10.1 years ago enricoferrero ▴ 680
0
votes
0
replies
2.3k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
10.2 years ago Jaritz,Markus ▴ 20
1
vote
2
replies
3.2k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 10.2 years ago by ★ 6.5k • written 10.2 years ago by ▴ 680
0
votes
2
replies
2.7k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
10.4 years ago • updated 10.3 years ago Tim Peters ▴ 230
0
votes
4
replies
3.4k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 2.2 years ago by • 0 • written 11.4 years ago by ★ 13k
0
votes
3
replies
3.2k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq Bsmooth
updated 2.2 years ago by • 0 • written 10.9 years ago by • 0
0
votes
2
replies
2.4k
views
bsmooth and bsseq for RRBS
bsseq bsseq
updated 12.0 years ago by ★ 4.2k • written 12.0 years ago by ★ 13k
1
vote
2
replies
1.8k
views
dmrFinder error
bsseq bsseq
updated 12.2 years ago by ★ 6.5k • written 12.2 years ago by ★ 13k
0
votes
1
reply
1.5k
views
bsseq in devel
bsseq bsseq
updated 12.5 years ago by ★ 4.2k • written 12.5 years ago by ★ 6.5k
0
votes
2
replies
2.5k
views
bsseq and BSmooth with RRBS
Sequencing bsseq Sequencing bsseq
updated 12.9 years ago by ★ 6.5k • written 12.9 years ago by ▴ 650
0
votes
1
reply
1.8k
views
Minimal input data format for bsseq
Sequencing Alignment bsseq Sequencing Alignment bsseq
updated 13.1 years ago by ★ 6.5k • written 13.1 years ago by ▴ 20
0
votes
0
replies
1.4k
views
[package announcement] bumphunter
charm minfi bsseq bumphunter charm minfi bsseq bumphunter
13.1 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.8k
views
Package announcement: bsseq
Sequencing Alignment Cancer Colon bsseq Sequencing Alignment Cancer Colon bsseq
13.5 years ago Kasper Daniel Hansen ★ 6.5k
38 results • Page 1 of 1
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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