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rnbeads
•
reset
4
votes
4
replies
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 8.1 years ago by
James W. MacDonald
65k • written 8.2 years ago by
AST
▴ 60
2
votes
9
replies
1.9k
views
Installation of RnBeads package fails on Ubuntu 18.04.5 LTS
RnBeads
updated 2.5 years ago by
j6163mls
• 0 • written 3.4 years ago by
vi.hammer
• 0
2
votes
4
replies
1.2k
views
How to launch the RnBeads Data Juggler?
RnBeads
3.2 years ago
Federica
▴ 10
2
votes
3
replies
1.1k
views
RnBeads::combine() - error?
RnBeads
Rnbeads2.0
RnBeads2
updated 3.1 years ago by
mscherer
▴ 50 • written 3.9 years ago by
D
▴ 10
2
votes
7
replies
2.1k
views
ggbio, RnBeads and 3.2.2
ggbio
rnbeads
rversion3.2.2
8.4 years ago
areyoujokingme
• 0
2
votes
4
replies
2.4k
views
Package RnBeads not available for R 3.1.2?
RnBeads
packages
R 3.1.2
8.8 years ago
bmreilly
• 0
1
vote
1
reply
846
views
How to export methylation tracks in bed format
RnBeads
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
Federica
▴ 10
1
vote
2
replies
1.5k
views
How to install Ghostscript in windows?
RnBeads.hg19
RnBeads
written 3.2 years ago by
Federica
▴ 10
1
vote
9
replies
2.2k
views
RnBeads fails with error in version 1.2 with GRanges v1.22.0
RnBeads
updated 8.5 years ago by
rnbeads
• 0 • written 8.5 years ago by
berger
• 0
1
vote
3
replies
1.2k
views
Obtaining annotated results from rnbeads
rnbeads
EPIC
updated 4.9 years ago by
mscherer
▴ 50 • written 4.9 years ago by
Mark Dunning
★ 1.1k
1
vote
1
reply
1.4k
views
Error in Rnbeads:Error in logger.error(em) : Could not create file. cannot popen '/usr/bin/which 'gs' 2>/dev/null', probable reason 'Cannot alloca…
R
bioconductor
rnbeads
microarray
illimina 450k methylation
6.5 years ago
preethibagopi28
▴ 10
1
vote
1
reply
1.7k
views
RnBeads - doesn't produce pdfs
rnbeads
illumina450k
updated 8.5 years ago by
pavlo.lutsik
▴ 10 • written 8.5 years ago by
Brian Smith
▴ 120
0
votes
0
replies
1.0k
views
'type = genes' for RnBeads::meth() function
rnbeads
7.2 years ago
Tom
▴ 10
0
votes
2
replies
2.1k
views
how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
minfi
RnBeads
noob
preprocessFunnorm
BMIQ
updated 7.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.1 years ago by
rahel14350
▴ 10
0
votes
0
replies
1.1k
views
Is it possible to use Rnbeads with WGBS data from epigenetics roadmap/ucsc data
rnbeads
wgbs
6.6 years ago
Theo
▴ 10
0
votes
1
reply
1.4k
views
RnBeads data preprocessing error
RnBeads
updated 6.1 years ago by
mlyall
• 0 • written 6.5 years ago by
Clyndas
• 0
0
votes
0
replies
1.0k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
6.2 years ago
gabrielrfries
• 0
0
votes
1
reply
1.1k
views
RnBeads "The analysis directory does not contain RnBSet objects"
rnbeads
6.0 years ago
neuro3030
• 0
0
votes
3
replies
1.1k
views
Trouble creating an RnBeads annotation for rn6 rat genome build
RnBeads
rn6
RnBeadsAnnotationCreator
updated 5.2 years ago by
mscherer
▴ 50 • written 5.2 years ago by
richardjacton
• 0
0
votes
2
replies
1.9k
views
RnBeads set ghost script environment variable
RnBeads
ghostscript
4.5 years ago
Kathrin.Klee
• 0
0
votes
0
replies
786
views
Is rnb.execute.import() has a bug in reading bismarkCytosine formart bed file? coordinates seem to be shifted by 1
RnBeads
4.0 years ago
caoy4g4
• 0
0
votes
0
replies
1.0k
views
How to get illumina CpG IDs by gene name?
MethylationArrayData
RnBeads
3.2 years ago
D
▴ 10
0
votes
0
replies
812
views
How to know the number of detected CpG islands with RnBeads
RnBeads
3.1 years ago
Federica
▴ 10
0
votes
0
replies
709
views
filtering options in RnBeads for array data
Epigenetics
RnBeads
MethylationArrayData
methylationArrayAnalysis
2.1 years ago
Jitendra
▴ 10
0
votes
0
replies
562
views
normalisation options in RnBeads
Epigenetics
RnBeads
R
Bioconducter
2.1 years ago
Jitendra
▴ 10
0
votes
0
replies
420
views
rnbeads inference
epigenetics
RnBeads
15 months ago
Jitendra
▴ 10
0
votes
3
replies
919
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 11 months ago by
Basti
▴ 780 • written 11 months ago by
Jitendra
▴ 10
0
votes
0
replies
2.2k
views
RnBeads check.names error:: "formal argument "check.names" matched by multiple actual arguments"
rnbeads
software error
8.4 years ago
areyoujokingme
• 0
0
votes
8
replies
1.9k
views
error in RnBeads installation
Epigenetics
RnBeads
R
2.1 years ago
Jitendra
▴ 10
0
votes
3
replies
3.0k
views
RnBeads cannot locate libjasper.so.1
rnbeads
gs
ghostscript
shared libraries
cluster
8.8 years ago
bmreilly
• 0
0
votes
2
replies
2.3k
views
error nonzero exit
illuminahumanmethylation450k.db
rnbeads
updated 8.2 years ago by
katwre
• 0 • written 8.7 years ago by
caroline.gluck
• 0
0
votes
1
reply
1.7k
views
RnBeads: Error in as.list.default(data.source) : no method for coercing this S4 class to a vector
rnbeads
error
as.vector(data)
s4vectors
s4
8.7 years ago • updated 8.6 years ago
schasse
• 0
0
votes
2
replies
1.7k
views
rnBeads error for the report path
software error
rnbeads
updated 8.6 years ago by
Dan Tenenbaum
★ 8.2k • written 8.6 years ago by
brenna.hott
• 0
0
votes
2
replies
1.9k
views
RnBeads - error with 'rnb.run.differential' module
RnBeads
illimina 450k methylation
8.5 years ago
Brian Smith
▴ 120
0
votes
1
reply
1.2k
views
RnBeads and technical replicates in differential analysis
rnbeads
replicates
updated 8.4 years ago by
rnbeads
• 0 • written 8.5 years ago by
Jon Manning
▴ 40
0
votes
1
reply
1.5k
views
RnBeads - test statistics for rnb.run.differential
RnBeads
updated 8.4 years ago by
rnbeads
• 0 • written 8.5 years ago by
Brian Smith
▴ 120
0
votes
2
replies
1.3k
views
RnBeads - save state between data crunching and report generation checkpoints within the differential methylation module?
rnbeads
xserver
headless-r
x11
8.2 years ago
areyoujokingme
• 0
0
votes
0
replies
1.5k
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads
methylation
illumina
epic microarray
7.7 years ago
rasii
• 0
0
votes
0
replies
1.0k
views
RnBeads, enrichment analysis
rnbeads
7.5 years ago
gaiusjaugustus
• 0
0
votes
0
replies
1.3k
views
Importing Infinium data files using RnBeads::rnb.execute.import()
RnBeads
7.4 years ago
Habil Zare
▴ 200
40 results • Page
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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…
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Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
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)
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