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
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
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
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 • updated 7.8 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 7.7 years ago by ▴ 240 • written 7.7 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 4.4 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
890
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
5.5 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
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
2
replies
958
views
MEDIPS - error using MEDIPS.CpGenrich
MEDIPS
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 5.4 years ago by ▴ 570 • written 5.4 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
963
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 9.9 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
832
views
MBD-seq non model species
MethylSeq ramwas MEDIPS qsea
updated 20 months ago by • 0 • written 21 months ago by ▴ 20
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
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Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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