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bsseq
•
reset
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
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
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
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
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
4
votes
8
replies
341
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 6 days ago by
Peter Hickey
▴ 740 • written 13 days ago by
Juan Higareda
• 0
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
Peter Hickey
▴ 740 • written 6.9 years ago by
Martin Aryee
▴ 20
1
vote
3
replies
1.9k
views
bsseq BSmooth error
bsseq
8.1 years ago
enricoferrero
▴ 660
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
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
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 19 months ago by
carla.geiger
• 0
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
1
vote
3
replies
1.3k
views
BSmooth: mclapply error when smoothing using BSmooth
bsseq
bsmooth
7.3 years ago
zuupcat
• 0
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
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
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
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
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
0
votes
1
reply
716
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
0
replies
717
views
DSS smoothing RRBS and strand collapse
DSS
BSSeq
4.1 years ago
stephanie.rialle
• 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
2
replies
840
views
Locating nearest genes in RRBS analysis
hiAnnotator
bsseq
DifferentialMethylation
edgeR
RRBSdata
23 months ago • updated 22 months ago
Mageiros
• 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
0
votes
1
reply
141
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 22 days ago by
James W. MacDonald
65k • written 24 days ago by
ja569116
• 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
1
reply
1.4k
views
Minimal input data format for bsseq
Sequencing
Alignment
bsseq
Sequencing
Alignment
bsseq
updated 11.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.3 years ago by
Martin Aryee
▴ 20
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
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
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
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
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
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
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
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
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
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
929
views
A few questions about BSseq package
bsseq
7.4 years ago
Stephen
• 0
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
38 results • Page
1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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