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DMRcate
•
reset
0
votes
0
replies
195
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate
Gviz
7 months ago
Ahdee
▴ 50
0
votes
1
reply
240
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 9 months ago by
James W. MacDonald
60k • written 9 months ago by
jfertaj
▴ 30
0
votes
2
replies
245
views
DMRcate: how to compare two comparisons and whether replicate is necessary
DMRcate
WGBS
biological_replicate
10 months ago
xie186
• 0
0
votes
6
replies
597
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 13 months ago by
Jovana Maksimovic
▴ 10 • written 2.1 years ago by
yoursbassanio
▴ 10
1
vote
2
replies
683
views
DMRcate extractRanges error
DMRcate
17 months ago
macsue.jacques
▴ 10
0
votes
0
replies
296
views
DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
20 months ago
Mike
▴ 10
3
votes
4
replies
375
views
Is it possible to run DMRcate directly with genomic positions instead of probe names?
DMRcate
updated 22 months ago by
Tim Peters
▴ 120 • written 22 months ago by
Jeni
• 0
0
votes
2
replies
349
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
2.0 years ago
zh9118
• 0
4
votes
9
replies
1.4k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
differencial methylation
updated 9 months ago by
jfertaj
▴ 30 • written 2.2 years ago by
Jeni
• 0
1
vote
8
replies
636
views
extract CpGs from DMRcate results
dmrcate
cpgs
results.ranges
DMRcate
updated 2.2 years ago by
Tim Peters
▴ 120 • written 2.2 years ago by
landenshanie
▴ 40
3
votes
5
replies
541
views
DMRcate: Cpgids in DMR
methylation
Epic
annotation
DMRcate
updated 2.8 years ago by
James W. MacDonald
60k • written 2.8 years ago by
yoursbassanio
▴ 10
0
votes
3
replies
461
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 3.0 years ago by
Tim Peters
▴ 120 • written 3.0 years ago by
anne-kristin.stavrum
• 0
0
votes
2
replies
545
views
cpg.annotate model requirements
DMRcate
ChAMP
updated 3.0 years ago by
Yuan Tian
▴ 250 • written 3.0 years ago by
kadm
• 0
1
vote
3
replies
638
views
DMRcate liftover to grch38
hg19
liftover
matrixeqtl
DMRcate
updated 3.2 years ago by
James W. MacDonald
60k • written 3.2 years ago by
yoursbassanio
▴ 10
2
votes
18
replies
3.2k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 4.1 years ago by
574233829
• 0 • written 6.2 years ago by
Giovanni Calice
▴ 160
0
votes
3
replies
857
views
DMRcate package :How to find the gene associated with coordinate
dmrcate
gene symbol
coordinate
4.1 years ago
574233829
• 0
2
votes
6
replies
1.0k
views
Bumphunting for longitudinal data
bumphunter
minfi
lmer
dmrcate
dmr analysis
updated 4.2 years ago by
Tim Peters
▴ 120 • written 4.3 years ago by
Ashlynn
• 0
0
votes
3
replies
1.1k
views
error in champ.DMR using DMRcate (v2.8.3)
champ
dmrcate
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 5.1 years ago by
Yuan Tian
▴ 90 • written 5.1 years ago by
mia
• 0
1
vote
2
replies
953
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate
dmrcate
methylation
updated 5.2 years ago by
Tim Peters
▴ 120 • written 5.2 years ago by
Ellen O
• 0
1
vote
3
replies
965
views
coef in dmrcate
dmrcate
bumphunter
methylation
epic
updated 5.3 years ago by
James W. MacDonald
60k • written 5.3 years ago by
yoursbassanio
▴ 10
0
votes
9
replies
2.3k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 5.3 years ago by
Tim Peters
▴ 120 • written 5.4 years ago by
Jenny Drnevich
★ 2.0k
1
vote
10
replies
2.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi
lumi
methylumi
dmrcate
illuminahumanmethylation450kanno.ilmn12.hg19
updated 5.4 years ago by
Tim Peters
▴ 120 • written 5.4 years ago by
poojitha.stemcell
▴ 10
0
votes
1
reply
1.0k
views
DMRcate: Scaling factor for bandwidth
dmrcate
dmr analysis
dmr
updated 5.5 years ago by
Tim Peters
▴ 120 • written 5.5 years ago by
alexandria.andrayas
▴ 10
0
votes
2
replies
890
views
DMRcate DMR.plot Turn Off Group Means
dmrcate
visualization
updated 5.6 years ago by
Tim Peters
▴ 120 • written 5.6 years ago by
csugai
• 0
1
vote
2
replies
680
views
DMRcate error in extractCoords function
software error
DMRcate
extractRanges
updated 5.6 years ago by
Tim Peters
▴ 120 • written 5.6 years ago by
Xavier Pastor
▴ 10
0
votes
1
reply
615
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 5.6 years ago by
Tim Peters
▴ 120 • written 5.6 years ago by
icobo
• 0
0
votes
9
replies
15k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 5.6 years ago by
Tim Peters
▴ 120 • written 5.8 years ago by
ew17
• 0
1
vote
15
replies
1.4k
views
DMRcate results meanpvals
dmrcate
updated 6.1 years ago by
Tim Peters
▴ 120 • written 6.1 years ago by
Giovanni Calice
▴ 160
0
votes
1
reply
595
views
conflicts in chromosome number
DMRcate
updated 6.1 years ago by
Tim Peters
▴ 120 • written 6.1 years ago by
yuping.zhang
• 0
2
votes
2
replies
1.2k
views
DMRcate error: object 'annotated' not found
dmrcate
error
updated 6.6 years ago by
Tim Peters
▴ 120 • written 6.6 years ago by
Eric Smith
• 0
0
votes
5
replies
1.4k
views
DMRcate cpg.annotate error: "Error in data.frame"
dmrcate
6.7 years ago
par.larsson
• 0
2
votes
2
replies
1.7k
views
DMRcate cpg.annotate error
dmrcate
design matrix
updated 6.7 years ago by
Tim Peters
▴ 120 • written 6.7 years ago by
Giovanni Calice
▴ 160
1
vote
1
reply
988
views
DMRcate: phenotype variable with multiple levels
dmr analysis
dmrcate
updated 7.0 years ago by
andrew.j.skelton73
▴ 360 • written 7.0 years ago by
irini.liampa
• 0
0
votes
3
replies
2.4k
views
DMRcate: incorporating covariates to find DMRs in methylation data?
limma
illimina 450k methylation
DMRcate
updated 7.3 years ago by
Tim Peters
▴ 120 • written 7.3 years ago by
Brian Smith
▴ 120
34 results • Page
1 of 1
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Replies
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Answer: spot- vs cell-level data access
by
Leonardo Collado Torres
▴ 1000
Hi, The `SingleCellExperiment` object you can download with `fetch_data(type = "sce")` pre-dates the creation of `SpatialExperiment`. No…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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