Showing : bsseq • reset
6
votes
5
replies
1.1k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 7 months ago by ▴ 740 • written 8 months ago by ▴ 20
0
votes
4
replies
1.8k
views
Error while smoothing BS-seq data with bsseq
bsseq
updated 7.0 years ago by • 0 • written 8.6 years ago by • 0
0
votes
3
replies
1.7k
views
Is there any way to set bsseq object as 'smoothed'?
bsseq bisulfite
8.0 years ago biohack92 • 0
0
votes
2
replies
845
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
23 months ago Mageiros • 0
0
votes
2
replies
2.1k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.6 years ago Tim Peters ▴ 170
1
vote
3
replies
1.4k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq bsmooth
7.3 years ago zuupcat • 0
0
votes
4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6 months ago by • 0 • written 9.6 years ago by ★ 13k
6
votes
14
replies
4.7k
views
How to correctly import Bismark coverage files into bsseq?
bsseq bismark methylation
8.4 years ago enricoferrero ▴ 660
1
vote
6
replies
1.7k
views
Unusually long running times for getMeth function since latest release
bsseq delayedarray
updated 6.8 years ago by ▴ 740 • written 6.8 years ago by ★ 1.9k
0
votes
3
replies
2.5k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq Bsmooth
updated 6 months ago by • 0 • written 9.2 years ago by • 0
7
votes
11
replies
3.5k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq dmr ttest pvalue
updated 8.2 years ago by 65k • written 8.2 years ago by ▴ 660
1
vote
2
replies
1.0k
views
Request to remove requirement for gr to have widths 1 in BSseq constructor
bsseq r package
updated 5.9 years ago by • 0 • written 5.9 years ago by ▴ 140
4
votes
8
replies
356
views
Memory errors using read.bismark?
dmrseq bsseq
updated 8 days ago by ▴ 740 • written 15 days ago by • 0
2
votes
3
replies
1.7k
views
bsseq combineList: how to get an HDF5Array-backed object as return value?
bsseq
updated 6.9 years ago by ▴ 740 • written 6.9 years ago by ▴ 20
0
votes
6
replies
1.8k
views
BSmooth 'names' attribute must be the same length as the vector
bsseq bsmooth
6.5 years ago ravi.tharakan • 0
7
votes
5
replies
1.8k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.0 years ago by ▴ 140
0
votes
3
replies
1.2k
views
Determination of Hypo- or Hyper- methylation
dmrseq bsseq
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
720
views
Varying results from DSS when specifying different BSobj
DSS DSS-single bsseq
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
0
votes
1
reply
1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.5 years ago by ▴ 10 • written 2.8 years ago by ▴ 80
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
0
votes
1
reply
1.4k
views
Minimal input data format for bsseq
Sequencing Alignment bsseq Sequencing Alignment bsseq
updated 11.4 years ago by ★ 6.5k • written 11.4 years ago by ▴ 20
0
votes
2
replies
1.9k
views
bsseq and BSmooth with RRBS
Sequencing bsseq Sequencing bsseq
updated 11.2 years ago by ★ 6.5k • written 11.2 years ago by ▴ 650
0
votes
1
reply
1.1k
views
bsseq in devel
bsseq bsseq
updated 10.8 years ago by ★ 4.2k • written 10.8 years ago by ★ 6.5k
4
votes
2
replies
1.4k
views
Bounded Regression with Limma for RRBS?
limma rrbs bsseq
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
1
vote
2
replies
1.5k
views
dmrFinder error
bsseq bsseq
updated 10.5 years ago by ★ 6.5k • written 10.5 years ago by ★ 13k
0
votes
2
replies
1.9k
views
bsmooth and bsseq for RRBS
bsseq bsseq
updated 10.3 years ago by ★ 4.2k • written 10.3 years ago by ★ 13k
0
votes
1
reply
1.3k
views
warning message with BSseq function
bsseq
updated 7.2 years ago by ★ 6.5k • written 7.2 years ago by • 0
0
votes
6
replies
1.9k
views
BSmooth error during the smoothing step for a subset of files
bsseq bsmooth
updated 7.1 years ago by ▴ 740 • written 7.1 years ago by • 0
0
votes
1
reply
145
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 24 days ago by 65k • written 26 days ago by • 0
0
votes
0
replies
1.1k
views
[package announcement] bumphunter
charm minfi bsseq bumphunter charm minfi bsseq bumphunter
11.4 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.9k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
8.5 years ago Jaritz,Markus ▴ 20
1
vote
0
replies
1.7k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
8.4 years ago enricoferrero ▴ 660
1
vote
3
replies
1.9k
views
bsseq BSmooth error
bsseq
8.1 years ago enricoferrero ▴ 660
0
votes
0
replies
1.0k
views
Does bsseq package work with technical replicates?
bsseq WGBS
7.4 years ago Welliton de Souza ▴ 70
0
votes
0
replies
934
views
A few questions about BSseq package
bsseq
7.4 years ago Stephen • 0
0
votes
0
replies
723
views
DSS smoothing RRBS and strand collapse
DSS BSSeq
4.1 years ago stephanie.rialle • 0
1
vote
3
replies
1.9k
views
read.bismark() ->Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
methylSig bsseq
updated 19 months ago by ▴ 740 • written 20 months ago by • 0
0
votes
0
replies
1.4k
views
Package announcement: bsseq
Sequencing Alignment Cancer Colon bsseq Sequencing Alignment Cancer Colon bsseq
11.7 years ago Kasper Daniel Hansen ★ 6.5k
38 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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