Showing : bumphunter • reset
6
votes
5
replies
1.3k
views
dmrseq installation failed
installation problem dmrseq bumphunter
updated 5.5 years ago by 3.8k • written 5.5 years ago by ▴ 10
6
votes
2
replies
4.2k
views
Plotting Differentially Methylated Regions
minfi bumphunter 450k region
updated 7.4 years ago by ▴ 80 • written 8.1 years ago by ▴ 40
4
votes
4
replies
3.0k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 7.3 years ago by 65k • written 7.3 years ago by • 0
4
votes
10
replies
2.9k
views
Using bumphunter with non-human genomes
bumphunter
updated 9.3 years ago by ★ 1.0k • written 9.5 years ago by ▴ 40
3
votes
5
replies
2.2k
views
bumphunter::annotateNearest with non-human genome
bumphunter
updated 9.3 years ago by ★ 1.0k • written 9.4 years ago by ▴ 40
3
votes
6
replies
2.1k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
updated 13 months ago by • 0 • written 8.8 years ago by ▴ 370
2
votes
6
replies
1.5k
views
bumphunter of multi covariates
bumphunter
7.7 years ago Asma rabe ▴ 290
2
votes
6
replies
1.8k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 6.0 years ago by ▴ 170 • written 6.0 years ago by • 0
2
votes
4
replies
1.4k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 4.9 years ago by ▴ 280 • written 4.9 years ago by ▴ 10
2
votes
1
reply
2.1k
views
News: Changes to matchGenes in bumphunter
annotation bumphunter News
updated 9.4 years ago by 41k • written 9.4 years ago by ▴ 60
2
votes
1
reply
1.7k
views
smoothing function in bumphunter in minfi
minfi bumphunter minfi bumphunter
updated 10.0 years ago by ★ 6.5k • written 10.0 years ago by ★ 13k
2
votes
8
replies
4.0k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 6.9 years ago by • 0 • written 7.0 years ago by ▴ 10
1
vote
5
replies
2.4k
views
Meaning of the value column in bumphunter output (minfi package)
minfi bumphunter
updated 6.1 years ago by • 0 • written 6.9 years ago by • 0
1
vote
2
replies
3.3k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO convert minfi bumphunter GO convert minfi bumphunter
updated 8.3 years ago by ▴ 30 • written 9.9 years ago by ★ 3.9k
1
vote
0
replies
1.2k
views
News: Bug found and fixed in bumphunter's bootstrap method
bumphunter News
8.5 years ago rafa ▴ 60
1
vote
9
replies
2.6k
views
bumphunter beta values
methylation minfi bumphunter
updated 8.0 years ago by 65k • written 8.0 years ago by ▴ 40
1
vote
4
replies
4.1k
views
bumphunter output clarification
bumphunter DMR DMR analysis minfi bioconductor
updated 7.3 years ago by ▴ 60 • written 7.3 years ago by • 0
1
vote
3
replies
1.5k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 10
1
vote
0
replies
1.3k
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
6.6 years ago Leonardo Collado Torres ★ 1.0k
0
votes
1
reply
1.6k
views
loessByCluster returning error in smooth function in bumphunter
bumphunter bumphunter
9.9 years ago Jiayi Sun ▴ 40
0
votes
3
replies
2.1k
views
smoothing function in bumphunter in minfi
minfi bumphunter minfi bumphunter
9.9 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
2
replies
2.1k
views
minfi release 1.8
SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter
updated 10.4 years ago by ★ 6.5k • written 10.4 years ago by ▴ 30
0
votes
1
reply
1.4k
views
minfi release 1.8
SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter
updated 10.4 years ago by ▴ 30 • written 10.4 years ago by ★ 6.5k
0
votes
5
replies
1.9k
views
bumphunter::matchGenes and all=TRUE
Annotation bumphunter Annotation bumphunter
updated 10.8 years ago by ★ 6.5k • written 10.8 years ago by ▴ 30
0
votes
0
replies
850
views
Bumphunter Output Details
bumphunter
9.0 years ago andrew.j.skelton73 ▴ 370
0
votes
0
replies
1.3k
views
How to format SWAN minfi data for bumphunter?
minfi bumphunter minfi bumphunter
10.8 years ago Guest User ★ 13k
0
votes
2
replies
845
views
Bumphunter output "regions" of 1 probe (L =1)
DMR bumphunter EPIC chip
4.2 years ago i.s.brorson • 0
0
votes
0
replies
1.1k
views
How to retrieve the (smoothed) baseline values from the bumphunting output object?
bumphunter
8.2 years ago fabian.schroeder • 0
0
votes
3
replies
1.7k
views
Bumphunter and minfi
genoset minfi bumphunter genoset minfi bumphunter
11.2 years ago Matthias Zilbauer ▴ 30
0
votes
0
replies
688
views
Does bump hunter support Infinium Mouse Methylation BeadChip Array data?
bumphunter
2.1 years ago ZHAOHUI • 0
0
votes
2
replies
1.1k
views
Runing into error while trying GRanges from R
rnaseq bumphunter genomicranges
7.8 years ago alva.james • 0
0
votes
3
replies
1.1k
views
minfi devel error
bumphunter
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 290
0
votes
4
replies
1.9k
views
Bumphunter output
bumphunter bumphunter
updated 11.2 years ago by ★ 6.5k • written 11.2 years ago by ▴ 400
0
votes
0
replies
1.1k
views
Bumphunter Algorithm Returns Regions with very few CpGs
bumphunter minfi
7.5 years ago graggsd • 0
0
votes
4
replies
2.2k
views
Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning and FWER calculations
minfi sva bumphunter
7.4 years ago • updated 7.3 years ago brhead ▴ 40
0
votes
1
reply
590
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
0
replies
1.1k
views
[package announcement] bumphunter
charm minfi bsseq bumphunter charm minfi bsseq bumphunter
11.4 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.4k
views
bumphunter P values and significance testing
minfi bumphunter
7.1 years ago cardenasca ▴ 40
0
votes
1
reply
1.6k
views
"Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter `matchGenes`
bumphunter
7.1 years ago jon.barenboim • 0
0
votes
3
replies
1.9k
views
Controlling for confounding variables in bumphunter
minfi bumphunter confounders
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
0
votes
3
replies
528
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 6 months ago by ▴ 770 • written 6 months ago by • 0
0
votes
3
replies
3.3k
views
Trying to use the liftOver function from the rtracklayer package in R 2.14.0
PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ★ 1.0k
0
votes
6
replies
3.0k
views
DMR identification: minfi speed, memory problems
Annotation convert minfi methyAnalysis bumphunter Annotation convert minfi methyAnalysis
updated 10.2 years ago by 65k • written 10.2 years ago by ★ 13k
0
votes
0
replies
696
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter minfi genomi
22 months ago runye • 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.1 years ago by • 0
0
votes
2
replies
1.4k
views
Bumphunter error: subscript out of bounds
bumphunter DMR doparallel multicore
updated 9 months ago by • 0 • written 6.0 years ago by • 0
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 65k • written 7.9 years ago by • 0
0
votes
3
replies
2.1k
views
Dependency installation error due to no longer available CRAN packages ('rngtools', 'pkgmaker')
installation minfi bumphunter
updated 5.9 years ago by ▴ 740 • written 6.0 years ago by • 0
0
votes
3
replies
1.9k
views
Paired samples and interactions models with bumphunter?
minfi bumphunter design and contrast matrix paired samples limma
8.3 years ago david.watson ▴ 30
0
votes
5
replies
3.4k
views
doParallel with Bumphunter gives Error in mcfork()
minfi bumphunter minfi bumphunter
updated 10.0 years ago by ★ 4.2k • written 10.0 years ago by ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none by Michael Love 41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Votes
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
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