Showing : MEDIPS • reset
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
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
4
votes
2
replies
1.4k
views
MEDIPS
MEDIPS MEDIPS
11.2 years ago Paolo Kunderfranco ▴ 350
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
3
votes
1
reply
1.2k
views
RMS question in MEDIPS
RMS RPKM MEDIPS
updated 6.2 years ago by ▴ 570 • written 6.2 years ago by ▴ 10
2
votes
13
replies
2.4k
views
Error with MEDIPS.createSet in queryHits
medips createset
8.5 years ago • updated 8.4 years ago Vanilla • 0
2
votes
1
reply
1.2k
views
How createSet from reduced "paire-ed" sequencing on MeDIPS?
medips R input files
updated 8.2 years ago by ▴ 570 • written 8.2 years ago by • 0
2
votes
1
reply
810
views
MEDIPS - Error in MEDIPS.CpGenrich
MEDIPS
updated 4.1 years ago by ▴ 570 • written 4.1 years ago by ▴ 20
2
votes
4
replies
890
views
MEDIPS results differ with sample ordering
MEDIPS edgeR
updated 4.0 years ago by ▴ 570 • written 4.3 years ago by ▴ 60
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
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
961
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
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
2
replies
1.5k
views
MEDIPS - RPKM
MEDIPS
9.1 years ago malbert1 • 0
1
vote
1
reply
727
views
MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 4.2 years ago by ▴ 570 • written 4.2 years ago by • 0
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
1
vote
1
reply
872
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 5.3 years ago by ▴ 570 • written 5.3 years ago by • 0
1
vote
1
reply
1.2k
views
Window size for MEDIPS
medips medip-seq peak finding luckas
updated 7.0 years ago by ▴ 570 • written 7.0 years ago by • 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
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
2
replies
1.5k
views
MEDIPS: Export rms values as Wiggle for visualization in UCSC
medips
9.5 years ago malbert1 • 0
1
vote
1
reply
1.5k
views
MeDIPS and use of the 'bwa' parameter
R medip-seq medips bwa
updated 7.7 years ago by ▴ 570 • written 7.7 years ago by • 0
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
1
vote
2
replies
939
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
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
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
0
replies
1.0k
views
It works: RE: using custom BSgenome with MEDIPS
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
10.4 years ago Vining, Kelly ▴ 220
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
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
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
764
views
error with MEDIPS.CpGenrich when using extend
MEDIPS MEDIPS
updated 12.5 years ago by ▴ 10 • written 12.5 years ago by ▴ 160
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
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
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
0
replies
2.1k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
10.4 years ago Hervé Pagès 16k
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
0
replies
760
views
Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray BSgenome BSgenome MEDIPS Microarray BSgenome BSgenome MEDIPS
11.2 years ago Stephen Turner ▴ 290
0
votes
0
replies
896
views
error with MEDIPS.CpGenrich -> resize + segfault in MEDIPS.plotCalibrationPlot
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
13.5 years ago Nora ▴ 20
0
votes
1
reply
1.3k
views
similar problem installing MEDIPS on Ubuntu 14.04
installation medips
7.5 years ago avilella ▴ 10
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
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
0
votes
1
reply
984
views
MEDIPS saturation error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 10.7 years ago by ▴ 40 • written 10.7 years ago by ★ 13k
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
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 9.6 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
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
0
votes
1
reply
1.1k
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
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
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
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
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
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Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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