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missmethyl
•
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0
votes
0
replies
89
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
16 days ago • updated 15 days ago
nurkenber
• 0
0
votes
1
reply
104
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 22 days ago by
James W. MacDonald
67k • written 22 days ago by
maximuscfyeung
• 0
0
votes
2
replies
277
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 23 days ago by
James W. MacDonald
67k • written 23 days ago by
maximuscfyeung
• 0
0
votes
2
replies
569
views
DMPs enrichment for MOUSE DNA methylation array
minfi
mCSEA
missme
missMethyl
updated 5 months ago by
nrenke
• 0 • written 5 months ago by
Lucie
• 0
1
vote
3
replies
1.6k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
11 months ago • updated 4 months ago
s.malik
• 0
0
votes
1
reply
813
views
dmrcate needs at least two non-NA values to interpolate
miss
DMRcate
missMethyl
updated 17 months ago by
Tim Peters
▴ 200 • written 17 months ago by
b.curran
• 0
0
votes
2
replies
840
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 10 months ago by
CHEN
• 0 • written 20 months ago by
Saanchi
• 0
1
vote
1
reply
812
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 21 months ago by
belinda.phipson
▴ 40 • written 21 months ago by
Grace
• 0
0
votes
1
reply
721
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
21 months ago
Grace
• 0
0
votes
0
replies
524
views
goMeth
missMethyl
22 months ago
anmolanp
▴ 10
2
votes
6
replies
1.3k
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 23 months ago by
belinda.phipson
▴ 40 • written 23 months ago by
Joana
• 0
2
votes
3
replies
1.5k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.1 years ago by
belinda.phipson
▴ 40 • written 2.1 years ago by
Lukas
• 0
0
votes
6
replies
1.6k
views
Find genes in pathways enrichment
dmrcate
enrichment analysis
epic array
goregion
missmethyl
updated 3.6 years ago by
Jovana Maksimovic
▴ 20 • written 4.5 years ago by
yoursbassanio
▴ 10
0
votes
1
reply
1.1k
views
missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 3.6 years ago by
Jovana Maksimovic
▴ 20 • written 4.4 years ago by
stewart999
▴ 10
1
vote
2
replies
2.3k
views
Minfi read.metharray.sheet error
minfi
methylation
dataimport
minfidata
missmethyl
updated 6.4 years ago by
James W. MacDonald
67k • written 6.4 years ago by
moldach
▴ 20
0
votes
0
replies
1.1k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
6.4 years ago
peter.fransquet
• 0
0
votes
0
replies
1.0k
views
missmethyl gsameth outputs matrix instead of dataframe
missmethyl
gsameth
6.6 years ago
owen.whitley
▴ 10
0
votes
1
reply
1.6k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 6.7 years ago by
lhuang7
▴ 50 • written 7.6 years ago by
Simone
▴ 190
0
votes
0
replies
1.1k
views
which value from ruvadj in missMethyl can present methylation status
methylation
missmethyl
RUV
batch effect
6.7 years ago
RC
• 0
0
votes
0
replies
1.1k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
6.7 years ago
Taub, Margaret
▴ 10
0
votes
2
replies
1.6k
views
prior.prob has opposite effects in goana and kegga?
limma
missMethyl
gometh
goana
kegga
updated 7.5 years ago by
Gordon Smyth
52k • written 7.7 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.5k
views
Details of gene names in DE
missmethyl
updated 7.8 years ago by
James W. MacDonald
67k • written 7.8 years ago by
r.clifford
• 0
0
votes
1
reply
1.4k
views
missMethyl package: gsameth bias plots
missmethyl
plots
bias
package
updated 7.9 years ago by
belinda.phipson
▴ 40 • written 7.9 years ago by
evani.radiya.dixit
• 0
1
vote
2
replies
1.7k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 8.5 years ago by
James W. MacDonald
67k • written 8.5 years ago by
graggsd
• 0
1
vote
3
replies
3.3k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
8.8 years ago
philipp24
▴ 30
3
votes
3
replies
3.9k
views
missMethyl: Gene ontology analysis
missMethyl
8.9 years ago • updated 8.8 years ago
philipp24
▴ 30
0
votes
0
replies
1.4k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
8.8 years ago
philipp24
▴ 30
27 results • Page
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Recent ...
Replies
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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