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Showing :
bumphunter
•
reset
0
votes
0
replies
202
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter
minfi
genomi
7 months ago
runye
• 0
0
votes
0
replies
311
views
Does bump hunter support Infinium Mouse Methylation BeadChip Array data?
bumphunter
11 months ago
ZHAOHUI
• 0
0
votes
9
replies
2.1k
views
clarification about bumphunter value output
minfi
bumphunter
written 4.9 years ago by
src3
• 0
0
votes
4
replies
452
views
Fix regions for bumphunter
bumphunter
DMR
methylation
minfi
3.0 years ago
i.s.brorson
• 0
0
votes
2
replies
418
views
Bumphunter output "regions" of 1 probe (L =1)
DMR
bumphunter
EPIC chip
3.0 years ago
i.s.brorson
• 0
0
votes
1
reply
618
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi
bumphunter
Rsamtools
3.6 years ago
Boran Gao
• 0
2
votes
4
replies
858
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 3.7 years ago by
Yuan Tian
▴ 250 • written 3.7 years ago by
rasmus.rydbirk
▴ 10
6
votes
5
replies
835
views
dmrseq installation failed
installation problem
dmrseq
bumphunter
updated 4.2 years ago by
shepherl
3.4k • written 4.3 years ago by
guy.bioinfo
▴ 10
0
votes
3
replies
1.7k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation
minfi
bumphunter
updated 4.7 years ago by
Peter Hickey
▴ 630 • written 4.7 years ago by
muellerf
• 0
2
votes
6
replies
1.2k
views
Bumphunting for longitudinal data
bumphunter
minfi
lmer
dmrcate
dmr analysis
updated 4.7 years ago by
Tim Peters
▴ 120 • written 4.7 years ago by
Ashlynn
• 0
0
votes
1
reply
822
views
Bumphunter error: subscript out of bounds
bumphunter
DMR
doparallel
multicore
4.7 years ago
arce.domingo.1407
• 0
1
vote
5
replies
1.7k
views
Meaning of the value column in bumphunter output (minfi package)
minfi
bumphunter
updated 4.9 years ago by
src3
• 0 • written 5.7 years ago by
Antonio M.
• 0
1
vote
0
replies
859
views
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
s4vectors
bumphunter
txdb.hsapiens.ucsc.hg38.knowngene
5.4 years ago
Leonardo Collado Torres
★ 1.0k
2
votes
8
replies
3.1k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter
minfi
loading error
rtracklayer
updated 5.7 years ago by
nilan666
• 0 • written 5.8 years ago by
juan-pablo.cerapio-arroyo
▴ 10
1
vote
3
replies
1.1k
views
coef in dmrcate
dmrcate
bumphunter
methylation
epic
updated 5.8 years ago by
James W. MacDonald
62k • written 5.8 years ago by
yoursbassanio
▴ 10
0
votes
3
replies
1.5k
views
Controlling for confounding variables in bumphunter
minfi
bumphunter
confounders
updated 5.9 years ago by
James W. MacDonald
62k • written 5.9 years ago by
gft219
• 0
0
votes
1
reply
1.2k
views
"Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter `matchGenes`
bumphunter
5.9 years ago
jon.barenboim
• 0
0
votes
0
replies
1.1k
views
bumphunter P values and significance testing
minfi
bumphunter
5.9 years ago
cardenasca
▴ 40
4
votes
4
replies
2.2k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation
dmr analysis
bumphunter
updated 6.1 years ago by
James W. MacDonald
62k • written 6.1 years ago by
chelsey.ju
• 0
1
vote
4
replies
3.0k
views
bumphunter output clarification
bumphunter
DMR
DMR analysis
minfi
bioconductor
updated 6.1 years ago by
rafa
▴ 60 • written 6.1 years ago by
chelsey.ju
• 0
0
votes
4
replies
1.6k
views
Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning and FWER calculations
minfi
sva
bumphunter
6.2 years ago • updated 6.1 years ago
brhead
▴ 40
6
votes
2
replies
3.3k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 6.2 years ago by
Dimitris Polychronopoulos
▴ 80 • written 6.9 years ago by
cardenasca
▴ 40
0
votes
0
replies
736
views
Bumphunter Algorithm Returns Regions with very few CpGs
bumphunter
minfi
6.3 years ago
graggsd
• 0
2
votes
6
replies
1.0k
views
bumphunter of multi covariates
bumphunter
6.5 years ago
Asma rabe
▴ 290
0
votes
3
replies
772
views
minfi devel error
bumphunter
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
Asma rabe
▴ 290
0
votes
2
replies
766
views
Runing into error while trying GRanges from R
rnaseq
bumphunter
genomicranges
6.6 years ago
alva.james
• 0
0
votes
1
reply
836
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 6.6 years ago by
James W. MacDonald
62k • written 6.6 years ago by
fleur_p90
• 0
1
vote
9
replies
2.1k
views
bumphunter beta values
methylation
minfi
bumphunter
updated 6.8 years ago by
James W. MacDonald
62k • written 6.8 years ago by
igor
▴ 40
0
votes
0
replies
789
views
How to retrieve the (smoothed) baseline values from the bumphunting output object?
bumphunter
7.0 years ago
fabian.schroeder
• 0
1
vote
2
replies
2.7k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO
convert
minfi
bumphunter
GO
convert
minfi
bumphunter
updated 7.0 years ago by
david.watson
▴ 20 • written 8.7 years ago by
Guido Hooiveld
★ 3.5k
0
votes
3
replies
1.5k
views
Paired samples and interactions models with bumphunter?
minfi
bumphunter
design and contrast matrix
paired samples
limma
7.0 years ago
david.watson
▴ 20
1
vote
0
replies
860
views
News:
Bug found and fixed in bumphunter's bootstrap method
bumphunter
News
7.3 years ago
rafa
▴ 60
3
votes
5
replies
1.4k
views
Complex Model Design with Bumphunter (Minfi)
minfi
bumphunter
model.matrix
linear model
7.6 years ago
andrew.j.skelton73
▴ 360
0
votes
0
replies
657
views
Bumphunter Output Details
bumphunter
7.8 years ago
andrew.j.skelton73
▴ 360
4
votes
10
replies
2.2k
views
Using bumphunter with non-human genomes
bumphunter
updated 8.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.2 years ago by
jessica.hekman
▴ 40
3
votes
5
replies
1.7k
views
bumphunter::annotateNearest with non-human genome
bumphunter
updated 8.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.2 years ago by
jessica.hekman
▴ 40
2
votes
1
reply
1.7k
views
News:
Changes to matchGenes in bumphunter
annotation
bumphunter
News
updated 8.2 years ago by
Michael Love
39k • written 8.2 years ago by
rafa
▴ 60
0
votes
3
replies
1.6k
views
smoothing function in bumphunter in minfi
minfi
bumphunter
minfi
bumphunter
8.7 years ago • updated 8.6 years ago
Kasper Daniel Hansen
6.5k
0
votes
1
reply
1.3k
views
loessByCluster returning error in smooth function in bumphunter
bumphunter
bumphunter
8.7 years ago
Jiayi Sun
▴ 40
0
votes
0
replies
1.1k
views
minfi release 1.8
SNP
Annotation
GO
probe
SNPlocs
PROcess
minfi
bumphunter
ChAMP
SNP
Annotation
GO
probe
8.7 years ago
swarmqq@gmail.com
▴ 10
2
votes
1
reply
1.4k
views
smoothing function in bumphunter in minfi
minfi
bumphunter
minfi
bumphunter
updated 8.7 years ago by
Kasper Daniel Hansen
6.5k • written 8.7 years ago by
Guest User
★ 12k
0
votes
5
replies
2.9k
views
doParallel with Bumphunter gives Error in mcfork()
minfi
bumphunter
minfi
bumphunter
updated 8.8 years ago by
Tim Triche
★ 4.2k • written 8.8 years ago by
Guest User
★ 12k
0
votes
0
replies
1.3k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
8.9 years ago
Allegra Petti
▴ 120
0
votes
6
replies
2.4k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
updated 8.9 years ago by
James W. MacDonald
62k • written 9.0 years ago by
Guest User
★ 12k
0
votes
12
replies
2.2k
views
bumphunter DMRs difficulties
PROcess
minfi
bumphunter
PROcess
minfi
bumphunter
updated 9.0 years ago by
Kasper Daniel Hansen
6.5k • written 9.0 years ago by
Giovanni Calice
▴ 160
0
votes
3
replies
1.4k
views
minfi release 1.8
SNP
Annotation
GO
probe
SNPlocs
PROcess
minfi
bumphunter
ChAMP
SNP
Annotation
GO
probe
updated 9.0 years ago by
Smeeta Shrestha
▴ 20 • written 9.0 years ago by
Tim Triche
★ 4.2k
0
votes
0
replies
1.1k
views
minfi release 1.8
SNP
Annotation
minfi
bumphunter
SNP
Annotation
minfi
bumphunter
9.0 years ago
C T
▴ 20
0
votes
2
replies
1.8k
views
minfi release 1.8
SNP
Annotation
minfi
bumphunter
SNP
Annotation
minfi
bumphunter
updated 9.2 years ago by
Kasper Daniel Hansen
6.5k • written 9.2 years ago by
Elmar Tobi
▴ 30
0
votes
1
reply
1.1k
views
minfi release 1.8
SNP
Annotation
minfi
bumphunter
SNP
Annotation
minfi
bumphunter
updated 9.2 years ago by
Elmar Tobi
▴ 30 • written 9.2 years ago by
Kasper Daniel Hansen
6.5k
0
votes
5
replies
1.5k
views
bumphunter::matchGenes and all=TRUE
Annotation
bumphunter
Annotation
bumphunter
updated 9.5 years ago by
Kasper Daniel Hansen
6.5k • written 9.5 years ago by
Anne Biton
▴ 30
50 results • Page
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I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
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