Showing : bsseq • reset
4
votes
8
replies
278
views
Memory errors using read.bismark?
dmrseq bsseq
updated 13 hours ago by ▴ 740 • written 7 days ago by • 0
0
votes
1
reply
125
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 15 days ago by 65k • written 17 days ago by • 0
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
1
vote
3
replies
1.8k
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 19 months ago by • 0
0
votes
2
replies
831
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
23 months ago • updated 22 months ago Mageiros • 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
0
votes
0
replies
708
views
DSS smoothing RRBS and strand collapse
DSS BSSeq
4.1 years ago stephanie.rialle • 0
0
votes
1
reply
709
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
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
1
vote
2
replies
995
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
7
votes
5
replies
1.8k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 5.9 years ago by ▴ 140
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
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
2
votes
3
replies
1.6k
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
4
replies
1.8k
views
Error while smoothing BS-seq data with bsseq
bsseq
updated 7.0 years ago by • 0 • written 8.5 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 7.0 years ago by ▴ 740 • written 7.1 years ago by • 0
0
votes
1
reply
1.3k
views
warning message with BSseq function
bsseq
updated 7.1 years ago by ★ 6.5k • written 7.1 years ago by • 0
1
vote
3
replies
1.3k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq bsmooth
7.3 years ago • updated 7.2 years ago zuupcat • 0
0
votes
0
replies
920
views
A few questions about BSseq package
bsseq
7.3 years ago Stephen • 0
0
votes
0
replies
1.0k
views
Does bsseq package work with technical replicates?
bsseq WGBS
7.4 years ago Welliton de Souza ▴ 70
4
votes
2
replies
1.4k
views
Bounded Regression with Limma for RRBS?
limma rrbs bsseq
updated 7.8 years ago by ★ 28k • written 7.9 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
1
vote
3
replies
1.8k
views
bsseq BSmooth error
bsseq
8.0 years ago enricoferrero ▴ 660
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
0
replies
1.6k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
8.4 years ago enricoferrero ▴ 660
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
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
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
2
replies
2.1k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.6 years ago Tim Peters ▴ 170
0
votes
4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 5 months ago by • 0 • written 9.6 years ago by ★ 13k
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 5 months ago by • 0 • written 9.1 years ago by • 0
0
votes
2
replies
1.9k
views
bsmooth and bsseq for RRBS
bsseq bsseq
updated 10.2 years ago by ★ 4.2k • written 10.2 years ago by ★ 13k
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
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
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
1.4k
views
Minimal input data format for bsseq
Sequencing Alignment bsseq Sequencing Alignment bsseq
updated 11.3 years ago by ★ 6.5k • written 11.3 years ago by ▴ 20
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
1.4k
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
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Replies
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Votes
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
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