Showing : medips • reset
7
votes
18
replies
3.0k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
2
votes
13
replies
2.4k
views
Error with MEDIPS.createSet in queryHits
medips createset
8.5 years ago Vanilla • 0
0
votes
9
replies
2.5k
views
MEDIPS: how does MEDIPS define a methylated region / cluster?
Sequencing MEDIPS
updated 9.6 years ago by • 0 • written 9.7 years ago by ★ 13k
0
votes
7
replies
1.6k
views
MEDIPS error extending reads
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ▴ 290
0
votes
6
replies
2.0k
views
MEDIPS: Number of windows tested in Paired-end data set
medips r
8.0 years ago peter.mcerlean • 0
0
votes
6
replies
1.7k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
0
votes
6
replies
1.9k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R medips medip-seq
7.7 years ago • updated 6.9 years ago stb • 0
0
votes
6
replies
1.6k
views
MEDIPS - input
MEDIPS input
7.9 years ago GFM ▴ 20
1
vote
6
replies
1.9k
views
MEDIP: Problem with MEDIPS.createSet
medips bsgenome medip-seq
updated 6.1 years ago by ▴ 570 • written 6.1 years ago by • 0
1
vote
6
replies
1.7k
views
MEDIPS: Output appears to be truncated
medips
updated 9.1 years ago by ▴ 570 • written 9.1 years ago by • 0
1
vote
6
replies
1.4k
views
Alternative methylation contexts with MEDIPS?
MEDIPS
updated 7.8 years ago by ▴ 240 • written 7.8 years ago by ▴ 90
0
votes
5
replies
1.6k
views
MEDIPS genome Vs createROIset significance issue
medips r
8.2 years ago peter.mcerlean • 0
0
votes
5
replies
1.9k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 220
0
votes
5
replies
2.1k
views
How does MEDIPS handle multiple mapping of a read
MEDIPS MEDIPS
updated 9.7 years ago by ▴ 570 • written 9.7 years ago by ★ 13k
4
votes
5
replies
1.3k
views
Extracting normalized counts in MEDIPS
MEDIPS MeDIP-seq
updated 2.6 years ago by ▴ 20 • written 4.5 years ago by ▴ 40
3
votes
5
replies
1.6k
views
CNV parameter not working - MEDIPS
medips medip-seq error lukas
updated 7.0 years ago by ▴ 240 • written 7.0 years ago by • 0
0
votes
5
replies
2.1k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 10.1 years ago by ▴ 570 • written 10.1 years ago by ▴ 220
2
votes
4
replies
893
views
MEDIPS results differ with sample ordering
MEDIPS edgeR
updated 4.0 years ago by ▴ 570 • written 4.3 years ago by ▴ 60
0
votes
4
replies
1.2k
views
I need BSgenome for Eucalyptus grandis
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ★ 13k
0
votes
4
replies
1.2k
views
CpG density in MEDIPS
CpG MEDIPS
5.5 years ago saripalligautam86 ▴ 10
1
vote
4
replies
1.1k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 19 months ago by • 0 • written 19 months ago by ▴ 20
0
votes
3
replies
1.4k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
0
votes
3
replies
1.3k
views
Caught segfault when running MEDIPS package
Sequencing MEDIPS Sequencing MEDIPS
updated 12.3 years ago by ▴ 40 • written 12.3 years ago by ★ 13k
0
votes
3
replies
2.9k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome
updated 10.7 years ago by ▴ 570 • written 10.7 years ago by ▴ 40
0
votes
3
replies
7.6k
views
Downgrading R to an older version
MEDIPS ChAMP MEDIPS ChAMP
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ▴ 70
0
votes
3
replies
1.3k
views
MEDIPS - Annotation output explanation
MEDIPS Output
6.0 years ago vjain • 0
0
votes
3
replies
1.1k
views
Coupling set error in MEDIPS
medips coupling set error cpg density
5.6 years ago saripalligautam86 ▴ 10
0
votes
2
replies
1.8k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 20
1
vote
2
replies
953
views
Read counts between QSEA and MEDIPs
qsea medips
updated 4.2 years ago by ▴ 240 • written 4.2 years ago by • 0
0
votes
2
replies
971
views
MEDIPS - error using MEDIPS.CpGenrich
MEDIPS
2.3 years ago • updated 2.2 years ago Ian • 0
0
votes
2
replies
1.5k
views
Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
0
votes
2
replies
1.1k
views
Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 11.2 years ago by ▴ 290 • written 11.2 years ago by ▴ 570
0
votes
2
replies
1.1k
views
create.set on MEDIPS
medips createset
updated 5.5 years ago by ▴ 570 • written 5.5 years ago by • 0
2
votes
2
replies
1.6k
views
Normalizing Depth Coverage between samples MEDIPS
normalization medips depth edgeR "R"
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
1
vote
2
replies
1.5k
views
MEDIPS - RPKM
MEDIPS
9.1 years ago malbert1 • 0
0
votes
2
replies
1.3k
views
New to R: How to use your own data for Bioconductor Packages
MEDIPS rsamtools
updated 8.7 years ago by ★ 8.2k • written 8.7 years ago by • 0
1
vote
2
replies
968
views
Comparing more than 2 experimental groups with MEDIPS?
medips medip-seq dna methylation dmr analysis
updated 5.4 years ago by ▴ 570 • written 5.4 years ago by • 0
0
votes
2
replies
1.3k
views
MEDIPS
Coverage MEDIPS Coverage MEDIPS
updated 10.6 years ago by ▴ 570 • written 10.6 years ago by ▴ 350
4
votes
2
replies
1.4k
views
MEDIPS
MEDIPS MEDIPS
11.2 years ago Paolo Kunderfranco ▴ 350
0
votes
2
replies
1.6k
views
Building custom genome in MeDIPS
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 11.6 years ago by 65k • written 11.6 years ago by ▴ 10
0
votes
2
replies
1.0k
views
MEDIPS no longer producing AMS values
Sequencing MEDIPS Sequencing MEDIPS
updated 10.7 years ago by ▴ 570 • written 10.7 years ago by ▴ 40
0
votes
2
replies
1.6k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 10.0 years ago by ▴ 240 • written 10.0 years ago by ▴ 10
1
vote
2
replies
1.5k
views
MEDIPS: Export rms values as Wiggle for visualization in UCSC
medips
9.5 years ago malbert1 • 0
0
votes
2
replies
1.4k
views
Bioconductor source code - Errno::ECONNREFUSED in Codes#show
medips bioconductor error source code
9.4 years ago malbert1 • 0
2
votes
2
replies
1.4k
views
Non-CpG Methylation in MEDIPS Package
medips
updated 9.1 years ago by ▴ 240 • written 9.1 years ago by • 0
0
votes
2
replies
1.7k
views
MeQA and MEDIPS
bioconductor meqa medips
updated 7.0 years ago by • 0 • written 8.0 years ago by • 0
0
votes
2
replies
1.2k
views
MEDIPS.createSet error
BSgenome BSgenome Rsamtools MEDIPS BSgenome BSgenome Rsamtools MEDIPS
updated 10.1 years ago by ▴ 570 • written 10.1 years ago by ▴ 220
1
vote
2
replies
2.2k
views
MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
p-value medips MACS
updated 8.9 years ago by ▴ 570 • written 8.9 years ago by • 0
0
votes
2
replies
1.3k
views
MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames?
MEDIPS mergeFrames
updated 9.0 years ago by ▴ 570 • written 9.0 years ago by • 0
0
votes
2
replies
836
views
MBD-seq non model species
MethylSeq ramwas MEDIPS qsea
updated 21 months ago by • 0 • written 21 months ago by ▴ 20
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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