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Showing :
bsseq
•
reset
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
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
James W. MacDonald
65k • written 8.2 years ago by
enricoferrero
▴ 660
4
votes
8
replies
356
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 8 days ago by
Peter Hickey
▴ 740 • written 15 days ago by
Juan Higareda
• 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
Peter Hickey
▴ 740 • written 7.1 years ago by
brandon.le
• 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
Peter Hickey
▴ 740 • written 6.8 years ago by
Alejandro Reyes
★ 1.9k
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
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
Peter Hickey
▴ 740 • written 8 months ago by
richardallenfriedmanbrooklyn
▴ 20
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
rcavalca
▴ 140
0
votes
4
replies
1.8k
views
Error while smoothing BS-seq data with bsseq
bsseq
updated 7.0 years ago by
Nikolay.Oskolkov
• 0 • written 8.6 years ago by
andreucat91
• 0
0
votes
4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage
bsseq
updated 6 months ago by
Adam
• 0 • written 9.6 years ago by
Guest User
★ 13k
1
vote
3
replies
1.9k
views
bsseq BSmooth error
bsseq
8.1 years ago
enricoferrero
▴ 660
1
vote
3
replies
1.4k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq
bsmooth
7.3 years ago
zuupcat
• 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
Peter Hickey
▴ 740 • written 6.9 years ago by
Martin Aryee
▴ 20
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
Adam
• 0 • written 9.2 years ago by
unmeshj
• 0
0
votes
3
replies
1.2k
views
Determination of Hypo- or Hyper- methylation
dmrseq
bsseq
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
Bruno Verstraeten
• 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
Peter Hickey
▴ 740 • written 20 months ago by
carla.geiger
• 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
1.9k
views
bsmooth and bsseq for RRBS
bsseq
bsseq
updated 10.3 years ago by
Tim Triche
★ 4.2k • written 10.3 years ago by
Guest User
★ 13k
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
2
replies
2.5k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 8.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.5 years ago by
enricoferrero
▴ 660
0
votes
2
replies
1.9k
views
bsseq and BSmooth with RRBS
Sequencing
bsseq
Sequencing
bsseq
updated 11.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.2 years ago by
Alex Gutteridge
▴ 650
4
votes
2
replies
1.4k
views
Bounded Regression with Limma for RRBS?
limma
rrbs
bsseq
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
nhejazi
• 0
1
vote
2
replies
1.5k
views
dmrFinder error
bsseq
bsseq
updated 10.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.5 years ago by
Guest User
★ 13k
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
emmascottgm
• 0 • written 5.9 years ago by
rcavalca
▴ 140
0
votes
1
reply
1.1k
views
bsseq in devel
bsseq
bsseq
updated 10.8 years ago by
Tim Triche
★ 4.2k • written 10.8 years ago by
Kasper Daniel Hansen
★ 6.5k
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
Kasper Daniel Hansen
★ 6.5k • written 11.4 years ago by
Martin Aryee
▴ 20
0
votes
1
reply
145
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 24 days ago by
James W. MacDonald
65k • written 26 days ago by
ja569116
• 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
James W. MacDonald
65k • written 4.5 years ago by
varunorama
• 0
0
votes
1
reply
1.1k
views
Gene level methylation values
methylation
methylKit
bsseq
updated 2.5 years ago by
alex.gos90
▴ 10 • written 2.8 years ago by
ag1805x
▴ 80
0
votes
1
reply
1.3k
views
warning message with BSseq function
bsseq
updated 7.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.2 years ago by
marie.trijau
• 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
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
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
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
38 results • Page
1 of 1
Recent ...
Replies
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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