Showing : MEDIPS • reset
0
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9
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2.5k
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MEDIPS: how does MEDIPS define a methylated region / cluster?
Sequencing MEDIPS
updated 9.6 years ago by • 0 • written 9.6 years ago by ★ 13k
0
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6
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1.6k
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MEDIPS - input
MEDIPS input
7.9 years ago • updated 7.8 years ago GFM ▴ 20
2
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13
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2.4k
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Error with MEDIPS.createSet in queryHits
medips createset
8.5 years ago • updated 8.4 years ago Vanilla • 0
0
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3
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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
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 3 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
0
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6
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1.9k
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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
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2
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1.7k
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MeQA and MEDIPS
bioconductor meqa medips
updated 7.0 years ago by • 0 • written 8.0 years ago by • 0
0
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5
replies
2.1k
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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
0
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2
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1.6k
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mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 9.9 years ago by ▴ 240 • written 9.9 years ago by ▴ 10
1
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2
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1.5k
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MEDIPS - RPKM
MEDIPS
9.1 years ago malbert1 • 0
2
votes
2
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1.4k
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Non-CpG Methylation in MEDIPS Package
medips
updated 9.1 years ago by ▴ 240 • written 9.1 years ago by • 0
0
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3
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1.4k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 220
0
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5
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1.6k
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MEDIPS genome Vs createROIset significance issue
medips r
8.2 years ago peter.mcerlean • 0
0
votes
3
replies
1.3k
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MEDIPS - Annotation output explanation
MEDIPS Output
6.0 years ago vjain • 0
1
vote
2
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1.4k
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MEDIPS: Export rms values as Wiggle for visualization in UCSC
medips
9.5 years ago malbert1 • 0
1
vote
6
replies
1.4k
views
Alternative methylation contexts with MEDIPS?
MEDIPS
updated 7.7 years ago by ▴ 240 • written 7.7 years ago by ▴ 90
0
votes
4
replies
1.2k
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CpG density in MEDIPS
CpG MEDIPS
5.5 years ago saripalligautam86 ▴ 10
2
votes
4
replies
878
views
MEDIPS results differ with sample ordering
MEDIPS edgeR
updated 4.0 years ago by ▴ 570 • written 4.2 years ago by ▴ 60
0
votes
2
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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
3
replies
1.1k
views
Coupling set error in MEDIPS
medips coupling set error cpg density
5.5 years ago saripalligautam86 ▴ 10
0
votes
1
reply
1.2k
views
MEDIPS
Sequencing Alignment MEDIPS Sequencing Alignment MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ▴ 350
0
votes
1
reply
762
views
error with MEDIPS.CpGenrich when using extend
MEDIPS MEDIPS
updated 12.5 years ago by ▴ 10 • written 12.5 years ago by ▴ 160
2
votes
2
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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
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 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 220
0
votes
1
reply
1.2k
views
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
2
replies
1.1k
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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
1
reply
1.3k
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Preprocessing BSgenome biomaRt BSgenome GenomicRanges MEDIPS Preprocessing BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ▴ 290
0
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1
reply
1.3k
views
similar problem installing MEDIPS on Ubuntu 14.04
installation medips
7.5 years ago avilella ▴ 10
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 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 220
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
0
votes
1
reply
1.0k
views
MEDIPS : Populating fragments from Paired End reads
medips
updated 9.1 years ago by ▴ 570 • written 9.1 years ago by • 0
0
votes
1
reply
1.2k
views
MEDIPS rms normalization by input
Coverage MEDIPS Coverage MEDIPS
updated 10.5 years ago by ▴ 570 • written 10.5 years ago by ★ 13k
0
votes
2
replies
1.3k
views
New to R: How to use your own data for Bioconductor Packages
MEDIPS rsamtools
updated 8.6 years ago by ★ 8.2k • written 8.6 years ago by • 0
0
votes
1
reply
1.1k
views
MEDIPS stable version problem
MEDIPS
updated 8.3 years ago by ▴ 570 • written 8.3 years ago by • 0
0
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2
replies
1.3k
views
MEDIPS
Coverage MEDIPS Coverage MEDIPS
updated 10.5 years ago by ▴ 570 • written 10.5 years ago by ▴ 350
4
votes
2
replies
1.4k
views
MEDIPS
MEDIPS MEDIPS
11.2 years ago Paolo Kunderfranco ▴ 350
4
votes
5
replies
1.3k
views
Extracting normalized counts in MEDIPS
MEDIPS MeDIP-seq
updated 2.6 years ago by ▴ 20 • written 4.4 years ago by ▴ 40
0
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3
replies
2.8k
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
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2
replies
1.0k
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MEDIPS no longer producing AMS values
Sequencing MEDIPS Sequencing MEDIPS
updated 10.7 years ago by ▴ 570 • written 10.7 years ago by ▴ 40
1
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2
replies
2.2k
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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
1
reply
1.9k
views
edgeR: Analyze mini-time-series MeDIP data of pooled DNAs without replicates?
Sequencing edgeR MEDIPS Sequencing edgeR MEDIPS
9.7 years ago Vang Le ▴ 80
0
votes
1
reply
1.7k
views
MEDIPS quality control
process medips
updated 9.5 years ago by ▴ 570 • written 9.6 years ago by • 0
0
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1
reply
1.3k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 9.7 years ago by ▴ 570 • written 9.7 years ago by ★ 13k
0
votes
1
reply
983
views
MEDIPS saturation error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 10.6 years ago by ▴ 40 • written 10.6 years ago by ★ 13k
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
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
0
votes
1
reply
2.0k
views
It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 10.0 years ago by ▴ 570 • written 10.1 years ago by ▴ 220
0
votes
1
reply
1.4k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 10.4 years ago by ▴ 240 • written 10.4 years ago by 16k
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
1
reply
965
views
How to use cutome reference genome?
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 11.7 years ago by ★ 6.5k • written 11.7 years ago by ★ 13k
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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 …
Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
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