Showing : BSSeq • reset
6
votes
5
replies
1.2k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 8 months ago by ▴ 740 • written 9 months ago by ▴ 20
0
votes
4
replies
1.9k
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
1.8k
views
Is there any way to set bsseq object as 'smoothed'?
bsseq bisulfite
8.1 years ago biohack92 • 0
0
votes
2
replies
865
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
2.0 years ago • updated 23 months ago Mageiros • 0
0
votes
2
replies
2.1k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.7 years ago Tim Peters ▴ 180
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
2.7k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6 months ago by • 0 • written 9.7 years ago by ★ 13k
6
votes
14
replies
4.8k
views
How to correctly import Bismark coverage files into bsseq?
bsseq bismark methylation
8.5 years ago • updated 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 6.9 years ago by ▴ 740 • written 6.9 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
3.6k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq dmr ttest pvalue
updated 8.3 years ago by 65k • written 8.3 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 6.0 years ago by • 0 • written 6.0 years ago by ▴ 140
4
votes
9
replies
489
views
Memory errors using read.bismark?
dmrseq bsseq
5 weeks ago • updated 10 days ago Juan Higareda • 0
2
votes
3
replies
1.7k
views
bsseq combineList: how to get an HDF5Array-backed object as return value?
bsseq
updated 7.0 years ago by ▴ 740 • written 7.0 years ago by ▴ 20
0
votes
6
replies
1.8k
views
BSmooth 'names' attribute must be the same length as the vector
bsseq bsmooth
6.6 years ago ravi.tharakan • 0
7
votes
5
replies
1.9k
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 6.0 years ago by 65k • written 6.0 years ago by • 0
0
votes
1
reply
735
views
Varying results from DSS when specifying different BSobj
DSS DSS-single bsseq
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
0
votes
1
reply
1.1k
views
Gene level methylation values
methylation methylKit bsseq
updated 2.6 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 8.6 years ago by ★ 6.5k • written 8.6 years ago by ▴ 660
0
votes
1
reply
1.5k
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 10.9 years ago by ★ 4.2k • written 10.9 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 10.6 years ago by ★ 6.5k • written 10.6 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 7.2 years ago by • 0
0
votes
1
reply
175
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
0
replies
1.1k
views
[package announcement] bumphunter
charm minfi bsseq bumphunter charm minfi bsseq bumphunter
11.5 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
7.5 years ago Welliton de Souza ▴ 70
0
votes
0
replies
951
views
A few questions about BSseq package
bsseq
7.4 years ago Stephen • 0
0
votes
0
replies
749
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 20 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
11.8 years ago Kasper Daniel Hansen ★ 6.5k
38 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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