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DNA Methylation
•
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0
votes
1
reply
940
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
4.2 years ago
grayapply2009
• 0
1
vote
2
replies
1.8k
views
WGCNA on methylation data
normalization
DNA methylation
WGCNA
updated 4.9 years ago by
Peter Langfelder
★ 3.0k • written 4.9 years ago by
enora.fremy
• 0
1
vote
2
replies
977
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.5 years ago by
Lukas Chavez
▴ 570 • written 5.5 years ago by
mtefit
• 0
7
votes
7
replies
1.6k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 5.6 years ago by
Sean Davis
21k • written 5.6 years ago by
RichardJActon
▴ 50
1
vote
2
replies
1.1k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
5.8 years ago
peter.fransquet
• 0
0
votes
0
replies
755
views
iEVORA wrapping up error
differential variability
dna methylation
iEVORA
DVP
6.1 years ago
poojitha.stemcell
▴ 10
0
votes
0
replies
1.1k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
6.3 years ago
gabrielrfries
• 0
0
votes
1
reply
1.1k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
ahmad.moousavi
• 0
2
votes
5
replies
1.8k
views
Error when prepare the TCGAdata
tcgabiolinks
dna methylation
updated 6.5 years ago by
Marcel Ramos
700 • written 6.5 years ago by
michaelwxf2012
• 0
1
vote
1
reply
1.5k
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 6.6 years ago by
James W. MacDonald
66k • written 6.6 years ago by
skids121
• 0
0
votes
0
replies
1.2k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV
minfi
preprocessing
dna methylation
7.2 years ago
Thomas
• 0
1
vote
2
replies
989
views
Correlating DNA methylation and Illumina gene expression microarray data
microarray
HM450
dna methylation
cohcap
updated 7.3 years ago by
James W. MacDonald
66k • written 7.3 years ago by
poojitha.stemcell
▴ 10
0
votes
1
reply
1.1k
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 7.9 years ago by
James W. MacDonald
66k • written 7.9 years ago by
fleur_p90
• 0
13 results • Page
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Replies
Comment: Slightly different count plots from R and spreadsheet
by
ATpoint
★ 4.1k
I don't think it is the purpose of the support site to debug Excel behaviour. The issue might be how it combines replicates into a single v…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
Karosham.Reddy
• 0
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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