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bsseq
•
reset
4
votes
9
replies
992
views
Memory errors using read.bismark?
dmrseq
bsseq
8 months ago • updated 7 months ago
Juan Higareda
• 0
0
votes
1
reply
494
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 8 months ago by
James W. MacDonald
67k • written 8 months ago by
ja569116
• 0
6
votes
5
replies
1.7k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 15 months ago by
Peter Hickey
▴ 740 • written 16 months ago by
richardallenfriedmanbrooklyn
▴ 30
1
vote
3
replies
2.4k
views
read.bismark() ->Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
methylSig
bsseq
updated 2.3 years ago by
Peter Hickey
▴ 740 • written 2.3 years ago by
carla.geiger
• 0
0
votes
2
replies
1.1k
views
Locating nearest genes in RRBS analysis
hiAnnotator
bsseq
DifferentialMethylation
edgeR
RRBSdata
2.6 years ago • updated 2.5 years ago
Mageiros
• 0
0
votes
1
reply
1.6k
views
Gene level methylation values
methylation
methylKit
bsseq
updated 3.2 years ago by
alex.gos90
▴ 10 • written 3.4 years ago by
Arindam
▴ 80
0
votes
0
replies
924
views
DSS smoothing RRBS and strand collapse
DSS
BSSeq
4.7 years ago
stephanie.rialle
• 0
0
votes
1
reply
923
views
Varying results from DSS when specifying different BSobj
DSS
DSS-single
bsseq
updated 5.1 years ago by
James W. MacDonald
67k • written 5.1 years ago by
varunorama
• 0
0
votes
3
replies
1.4k
views
Determination of Hypo- or Hyper- methylation
dmrseq
bsseq
updated 6.5 years ago by
James W. MacDonald
67k • written 6.5 years ago by
Bruno Verstraeten
• 0
1
vote
2
replies
1.2k
views
Request to remove requirement for gr to have widths 1 in BSseq constructor
bsseq
r
package
updated 6.6 years ago by
emmascottgm
• 0 • written 6.6 years ago by
rcavalca
▴ 140
7
votes
5
replies
2.1k
views
Strange error in bsseq when trying to assign seqinfo
bsseq
genomeinfodb
genomicranges
seqinfo
written 6.6 years ago by
rcavalca
▴ 140
0
votes
6
replies
2.1k
views
BSmooth 'names' attribute must be the same length as the vector
bsseq
bsmooth
7.1 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 7.4 years ago by
Peter Hickey
▴ 740 • written 7.4 years ago by
Alejandro Reyes
★ 1.9k
2
votes
3
replies
1.9k
views
bsseq combineList: how to get an HDF5Array-backed object as return value?
bsseq
updated 7.5 years ago by
Peter Hickey
▴ 740 • written 7.5 years ago by
Martin Aryee
▴ 20
0
votes
4
replies
2.1k
views
Error while smoothing BS-seq data with bsseq
bsseq
updated 7.6 years ago by
Nikolay.Oskolkov
• 0 • written 9.2 years ago by
andreucat91
• 0
0
votes
6
replies
2.3k
views
BSmooth error during the smoothing step for a subset of files
bsseq
bsmooth
updated 7.7 years ago by
Peter Hickey
▴ 740 • written 7.7 years ago by
brandon.le
• 0
0
votes
1
reply
1.5k
views
warning message with BSseq function
bsseq
updated 7.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.8 years ago by
marie.trijau
• 0
1
vote
3
replies
1.5k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq
bsmooth
7.9 years ago
zuupcat
• 0
0
votes
0
replies
1.1k
views
A few questions about BSseq package
bsseq
8.0 years ago
Stephen
• 0
0
votes
0
replies
1.2k
views
Does bsseq package work with technical replicates?
bsseq
WGBS
8.0 years ago
Welliton de Souza
▴ 70
4
votes
2
replies
1.6k
views
Bounded Regression with Limma for RRBS?
limma
rrbs
bsseq
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
nhejazi
• 0
0
votes
3
replies
2.0k
views
Is there any way to set bsseq object as 'smoothed'?
bsseq
bisulfite
8.6 years ago
biohack92
• 0
1
vote
3
replies
2.1k
views
bsseq BSmooth error
bsseq
8.7 years ago
enricoferrero
▴ 660
7
votes
11
replies
4.1k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq
dmr
ttest
pvalue
updated 8.8 years ago by
James W. MacDonald
67k • written 8.8 years ago by
enricoferrero
▴ 660
1
vote
0
replies
1.8k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
9.0 years ago
enricoferrero
▴ 660
6
votes
14
replies
5.5k
views
How to correctly import Bismark coverage files into bsseq?
bsseq
bismark
methylation
9.0 years ago
enricoferrero
▴ 660
0
votes
0
replies
2.1k
views
Job:
Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq
atac-seq
gro-seq
bsseq
rnaseq
Job
9.1 years ago
Jaritz,Markus
▴ 20
1
vote
2
replies
2.8k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 9.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.1 years ago by
enricoferrero
▴ 660
0
votes
2
replies
2.4k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS
bsseq
summarizedexperiment
9.3 years ago • updated 9.2 years ago
Tim Peters
▴ 200
0
votes
4
replies
3.0k
views
Error using Bsmooth.tstat due to NAs
Coverage
bsseq
updated 13 months ago by
Adam
• 0 • written 10.2 years ago by
Guest User
★ 13k
0
votes
3
replies
2.8k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq
Bsmooth
updated 13 months ago by
Adam
• 0 • written 9.8 years ago by
unmeshj
• 0
0
votes
2
replies
2.1k
views
bsmooth and bsseq for RRBS
bsseq
bsseq
updated 10.9 years ago by
Tim Triche
★ 4.2k • written 10.9 years ago by
Guest User
★ 13k
1
vote
2
replies
1.6k
views
dmrFinder error
bsseq
bsseq
updated 11.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.1 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
bsseq in devel
bsseq
bsseq
updated 11.4 years ago by
Tim Triche
★ 4.2k • written 11.4 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
2
replies
2.2k
views
bsseq and BSmooth with RRBS
Sequencing
bsseq
Sequencing
bsseq
updated 11.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.8 years ago by
Alex Gutteridge
▴ 650
0
votes
1
reply
1.6k
views
Minimal input data format for bsseq
Sequencing
Alignment
bsseq
Sequencing
Alignment
bsseq
updated 12.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.0 years ago by
Martin Aryee
▴ 20
0
votes
0
replies
1.2k
views
[package announcement] bumphunter
charm
minfi
bsseq
bumphunter
charm
minfi
bsseq
bumphunter
12.0 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
12.4 years ago
Kasper Daniel Hansen
★ 6.5k
38 results • Page
1 of 1
Recent ...
Replies
Answer: RSubread output significantly different from bash Subread output
by
Gordon Smyth
52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
by
Michael Love
43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores
by
gabriel.hoffman
▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output
by
Aimee
• 0
Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back. Update: This completely resolve…
Answer: RSubread output significantly different from bash Subread output
by
ATpoint
★ 4.6k
The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
Awards
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Teacher
to
Michael Love
43k
Popular Question
to
Dario Strbenac
★ 1.5k
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to
ATpoint
★ 4.6k
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to
Gordon Smyth
52k
Popular Question
to
bhandary.8590
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