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methylkit
•
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0
votes
1
reply
118
views
Granges regionCounts not returning the expected number of entries
methylKit
21 days ago • updated 20 days ago
Modoc Kesner
▴ 10
1
vote
2
replies
204
views
MethylKit read issue
methylKit
updated 20 days ago by
James W. MacDonald
65k • written 25 days ago by
CHEN
• 0
0
votes
0
replies
432
views
MethylKit::calculateDiffMeth with two experimental factors
methylKit
8 months ago
Andrés
• 0
0
votes
1
reply
582
views
[Methylkit]-Error in validObject(.Object) :
methRead
methylkit
16 months ago
liulip
• 0
0
votes
0
replies
646
views
Generating 5mCG or 5hmCG values per gene from BS/OXBS data
methyl
methylKit
2.1 years ago
hasche
• 0
0
votes
6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges
methylKit
S4Vectors
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
hasche
• 0
0
votes
1
reply
1.1k
views
Methread error Error in data[, 5] * data[, 6] : non-numeric argument to binary operator
methylkit
updated 2.5 years ago by
alex.gos90
▴ 10 • written 2.9 years ago by
hasche
• 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
2
votes
1
reply
1.1k
views
Not able to Annotate CpG Island using methylKit
annotateWithGeneParts
methylKit
2.6 years ago
tanmayroy1979
▴ 20
0
votes
2
replies
1.2k
views
normalizecoverage in methylkit outputs NAs
methylkit
normalizecoverage
NA
updated 5.5 years ago by
altuna akalin
▴ 20 • written 5.5 years ago by
GFM
▴ 20
0
votes
2
replies
1.1k
views
MethylKit DSS Package
R
bioconductor
methylation
methylkit
updated 5.8 years ago by
altuna akalin
▴ 20 • written 5.8 years ago by
nilaycan
• 0
0
votes
3
replies
1.6k
views
How to install MethylKit?
methylkit
Tutorial
updated 6.4 years ago by
Martin Morgan
25k • written 6.4 years ago by
s1432985
• 0
0
votes
2
replies
1.7k
views
report error of methylkit
methylKit
updated 6.8 years ago by
altuna akalin
▴ 20 • written 6.8 years ago by
ch8316f5eyu
• 0
0
votes
2
replies
1.7k
views
error reading bismark sam/bam files
methylKit
6.9 years ago
kamal.fartiyal84
▴ 10
0
votes
4
replies
1.6k
views
load methylKit segfault error
methylKit
bioconductor
updated 7.7 years ago by
Martin Morgan
25k • written 7.7 years ago by
tangming2005
▴ 190
15 results • Page
1 of 1
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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