Showing : bsseq • reset
4
votes
9
replies
1.2k
views
Memory errors using read.bismark?
dmrseq bsseq
10 months ago Juan Higareda • 0
0
votes
1
reply
629
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 11 months ago by 68k • written 11 months ago by • 0
6
votes
5
replies
1.9k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 18 months ago by ▴ 750 • written 19 months ago by ▴ 30
1
vote
3
replies
2.6k
views
read.bismark() ->Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
methylSig bsseq
updated 2.5 years ago by ▴ 750 • written 2.5 years ago by • 0
0
votes
2
replies
1.2k
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
2.8 years ago • updated 2.7 years ago Mageiros • 0
0
votes
1
reply
1.9k
views
Gene level methylation values
methylation methylKit bsseq
updated 3.4 years ago by ▴ 10 • written 3.6 years ago by ▴ 80
0
votes
0
replies
981
views
DSS smoothing RRBS and strand collapse
DSS BSSeq
4.9 years ago stephanie.rialle • 0
0
votes
1
reply
987
views
Varying results from DSS when specifying different BSobj
DSS DSS-single bsseq
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
votes
3
replies
1.5k
views
Determination of Hypo- or Hyper- methylation
dmrseq bsseq
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
1
vote
2
replies
1.3k
views
Request to remove requirement for gr to have widths 1 in BSseq constructor
bsseq r package
updated 6.8 years ago by • 0 • written 6.8 years ago by ▴ 140
7
votes
5
replies
2.2k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.8 years ago by ▴ 140
0
votes
6
replies
2.2k
views
BSmooth 'names' attribute must be the same length as the vector
bsseq bsmooth
7.4 years ago ravi.tharakan • 0
1
vote
6
replies
2.0k
views
Unusually long running times for getMeth function since latest release
bsseq delayedarray
updated 7.7 years ago by ▴ 750 • written 7.7 years ago by ★ 1.9k
2
votes
3
replies
2.0k
views
bsseq combineList: how to get an HDF5Array-backed object as return value?
bsseq
updated 7.7 years ago by ▴ 750 • written 7.7 years ago by ▴ 20
0
votes
4
replies
2.2k
views
Error while smoothing BS-seq data with bsseq
bsseq
updated 7.8 years ago by • 0 • written 9.4 years ago by • 0
0
votes
6
replies
2.4k
views
BSmooth error during the smoothing step for a subset of files
bsseq bsmooth
updated 7.9 years ago by ▴ 750 • written 7.9 years ago by • 0
0
votes
1
reply
1.5k
views
warning message with BSseq function
bsseq
updated 8.0 years ago by ★ 6.5k • written 8.0 years ago by • 0
1
vote
3
replies
1.6k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq bsmooth
8.1 years ago zuupcat • 0
0
votes
0
replies
1.2k
views
A few questions about BSseq package
bsseq
8.2 years ago Stephen • 0
0
votes
0
replies
1.2k
views
Does bsseq package work with technical replicates?
bsseq WGBS
8.3 years ago Welliton de Souza ▴ 70
4
votes
2
replies
1.7k
views
Bounded Regression with Limma for RRBS?
limma rrbs bsseq
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
3
replies
2.1k
views
Is there any way to set bsseq object as 'smoothed'?
bsseq bisulfite
8.9 years ago biohack92 • 0
1
vote
3
replies
2.2k
views
bsseq BSmooth error
bsseq
8.9 years ago enricoferrero ▴ 680
7
votes
11
replies
4.3k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq dmr ttest pvalue
updated 9.1 years ago by 68k • written 9.1 years ago by ▴ 680
1
vote
0
replies
1.9k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
9.2 years ago enricoferrero ▴ 680
6
votes
14
replies
5.8k
views
How to correctly import Bismark coverage files into bsseq?
bsseq bismark methylation
9.3 years ago • updated 9.2 years ago enricoferrero ▴ 680
0
votes
0
replies
2.1k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
9.3 years ago Jaritz,Markus ▴ 20
1
vote
2
replies
2.9k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 9.4 years ago by ★ 6.5k • written 9.4 years ago by ▴ 680
0
votes
2
replies
2.4k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
9.5 years ago Tim Peters ▴ 230
0
votes
4
replies
3.1k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 16 months ago by • 0 • written 10.5 years ago by ★ 13k
0
votes
3
replies
2.9k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq Bsmooth
updated 16 months ago by • 0 • written 10.0 years ago by • 0
0
votes
2
replies
2.2k
views
bsmooth and bsseq for RRBS
bsseq bsseq
updated 11.1 years ago by ★ 4.2k • written 11.1 years ago by ★ 13k
1
vote
2
replies
1.7k
views
dmrFinder error
bsseq bsseq
updated 11.3 years ago by ★ 6.5k • written 11.4 years ago by ★ 13k
0
votes
1
reply
1.3k
views
bsseq in devel
bsseq bsseq
updated 11.7 years ago by ★ 4.2k • written 11.7 years ago by ★ 6.5k
0
votes
2
replies
2.2k
views
bsseq and BSmooth with RRBS
Sequencing bsseq Sequencing bsseq
updated 12.0 years ago by ★ 6.5k • written 12.0 years ago by ▴ 650
0
votes
1
reply
1.7k
views
Minimal input data format for bsseq
Sequencing Alignment bsseq Sequencing Alignment bsseq
updated 12.2 years ago by ★ 6.5k • written 12.2 years ago by ▴ 20
0
votes
0
replies
1.3k
views
[package announcement] bumphunter
charm minfi bsseq bumphunter charm minfi bsseq bumphunter
12.3 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.6k
views
Package announcement: bsseq
Sequencing Alignment Cancer Colon bsseq Sequencing Alignment Cancer Colon bsseq
12.6 years ago Kasper Daniel Hansen ★ 6.5k
38 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
Locations • All
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