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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 8.1 years ago by
AST
▴ 60
2
votes
9
replies
1.8k
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
3.1 years ago
Federica
▴ 10
2
votes
3
replies
1.1k
views
RnBeads::combine() - error?
RnBeads
Rnbeads2.0
RnBeads2
updated 3.0 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
840
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 3.1 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 8.4 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
6.4 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 7.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.0 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
1.3k
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
776
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
3.1 years ago
D
▴ 10
0
votes
0
replies
804
views
How to know the number of detected CpG islands with RnBeads
RnBeads
3.1 years ago
Federica
▴ 10
0
votes
0
replies
698
views
filtering options in RnBeads for array data
Epigenetics
RnBeads
MethylationArrayData
methylationArrayAnalysis
2.1 years ago
Jitendra
▴ 10
0
votes
0
replies
549
views
normalisation options in RnBeads
Epigenetics
RnBeads
R
Bioconducter
2.1 years ago
Jitendra
▴ 10
0
votes
0
replies
415
views
rnbeads inference
epigenetics
RnBeads
14 months ago
Jitendra
▴ 10
0
votes
3
replies
902
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 11 months ago by
Basti
▴ 770 • 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
1.8k
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
8.7 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
8.6 years ago
schasse
• 0
0
votes
2
replies
1.7k
views
rnBeads error for the report path
software error
rnbeads
updated 8.5 years ago by
Dan Tenenbaum
★ 8.2k • written 8.5 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 • updated 8.4 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 8.4 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 8.4 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
7.6 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
1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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