Showing : MEDIPS • reset
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Batch Correction while implementing QSEA package
qsea MEDIPS MEDIPSData DNAMethylation
9 weeks ago User3088 • 0
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0
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360
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medips-output
ngsReports MEDIPS
13 months ago Researcher ▴ 10
9
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18
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4.0k
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Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 15 months ago by ▴ 280 • written 8.0 years ago by ▴ 20
0
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1
reply
479
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MEDIPS - covariate
MEDIPS
updated 17 months ago by 68k • written 17 months ago by • 0
0
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0
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489
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CpG coverage with MEDIPS
MEDIPS CpG
19 months ago greta • 0
0
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0
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771
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How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.2 years ago Luomeng • 0
1
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4
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1.6k
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QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 2.5 years ago by • 0 • written 2.6 years ago by ▴ 20
0
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2
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1.1k
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MBD-seq non model species
MethylSeq ramwas MEDIPS qsea
updated 2.7 years ago by • 0 • written 2.7 years ago by ▴ 20
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3
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1.4k
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MEDIPS - error using MEDIPS.CpGenrich
MEDIPS
updated 7 weeks ago by • 0 • written 3.2 years ago by • 0
0
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0
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955
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MEDIPS.meth output
MEDIPS edgeR l
3.6 years ago Aranzazu • 0
0
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0
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823
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MEDIPS - export wig with normalized counts
MEDIPS
4.1 years ago lshepard ▴ 40
2
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4
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1.2k
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MEDIPS results differ with sample ordering
MEDIPS edgeR
updated 4.9 years ago by ▴ 570 • written 5.2 years ago by ▴ 60
2
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1
reply
1.0k
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MEDIPS - Error in MEDIPS.CpGenrich
MEDIPS
updated 5.1 years ago by ▴ 570 • written 5.1 years ago by ▴ 20
1
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1
reply
927
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MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 5.1 years ago by ▴ 570 • written 5.1 years ago by • 0
1
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2
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1.3k
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Read counts between QSEA and MEDIPs
qsea medips
updated 5.1 years ago by ▴ 280 • written 5.1 years ago by • 0
4
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5
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1.7k
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Extracting normalized counts in MEDIPS
MEDIPS MeDIP-seq
updated 3.5 years ago by ▴ 20 • written 5.4 years ago by ▴ 40
0
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0
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852
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Why does MEDIPS only import read 1 when paired=TRUE for MEDIPS.createSet()function ?
#MEDIPS MEDIPS
5.4 years ago agm • 0
1
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1
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1.1k
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sva correction for MEDIPS
MEDIPS svaseq sva
updated 6.2 years ago by ▴ 570 • written 6.2 years ago by • 0
0
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0
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1.2k
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error importing bam file for MEDIPS analysis
MEDIPS bamfile
updated 6.2 years ago by 0 • written 6.4 years ago by • 0
1
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2
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1.2k
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Comparing more than 2 experimental groups with MEDIPS?
medips medip-seq dna methylation dmr analysis
updated 6.4 years ago by ▴ 570 • written 6.4 years ago by • 0
0
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2
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1.4k
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create.set on MEDIPS
medips createset
updated 6.4 years ago by ▴ 570 • written 6.4 years ago by • 0
0
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4
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1.6k
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CpG density in MEDIPS
CpG MEDIPS
6.5 years ago saripalligautam86 ▴ 10
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0
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1.3k
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Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools QSEA MEDIPS
6.5 years ago saripalligautam86 ▴ 10
0
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3
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1.4k
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Coupling set error in MEDIPS
medips coupling set error cpg density
6.5 years ago saripalligautam86 ▴ 10
0
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0
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858
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CouplingSet error in MeDIPS
MEDIPS coupling set error
6.5 years ago saripalligautam86 ▴ 10
0
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3
replies
1.6k
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MEDIPS - Annotation output explanation
MEDIPS Output
6.9 years ago vjain • 0
1
vote
6
replies
2.4k
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MEDIP: Problem with MEDIPS.createSet
medips bsgenome medip-seq
updated 7.1 years ago by ▴ 570 • written 7.1 years ago by • 0
3
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1
reply
1.4k
views
RMS question in MEDIPS
RMS RPKM MEDIPS
updated 7.1 years ago by ▴ 570 • written 7.1 years ago by ▴ 10
0
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6
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2.3k
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MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R medips medip-seq
8.7 years ago • updated 7.8 years ago stb • 0
3
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5
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2.0k
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CNV parameter not working - MEDIPS
medips medip-seq error lukas
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
1
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1
reply
1.5k
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Window size for MEDIPS
medips medip-seq peak finding luckas
updated 7.9 years ago by ▴ 570 • written 7.9 years ago by • 0
0
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2
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1.9k
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MeQA and MEDIPS
bioconductor meqa medips
updated 7.9 years ago by • 0 • written 8.9 years ago by • 0
0
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1
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1.3k
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How does the function MEDIPS.CpGenrich work?
medips
updated 8.0 years ago by ▴ 570 • written 8.0 years ago by • 0
0
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1
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1.7k
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Error raised during execution of MEDIPS package
medips
updated 8.1 years ago by ▴ 570 • written 8.1 years ago by • 0
0
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1
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1.2k
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MEDIPS: case study with different replicate numbers of control and case
MEDIPS
updated 8.2 years ago by ▴ 570 • written 8.2 years ago by • 0
0
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1
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1.4k
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Insertion size when using 'paired' in MEDIPS.createSet()
medips R medip-seq pair-end reads
updated 8.3 years ago by ▴ 570 • written 8.3 years ago by • 0
0
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1
reply
1.3k
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How to make my custom genome available in MEDIPS?
MEDIPS
8.4 years ago Vijay Lakhujani • 0
0
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1
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1.5k
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similar problem installing MEDIPS on Ubuntu 14.04
installation medips
8.5 years ago avilella ▴ 10
0
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1
reply
1.4k
views
MEDIPS - do reads without CG's get filtered out prior to analysis?
medips
updated 8.5 years ago by ▴ 570 • written 8.5 years ago by • 0
0
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1
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1.3k
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How does the 'paired' argument works in MeDIPS 1.23.2
medips medip-seq R pair-end reads
updated 8.6 years ago by ▴ 570 • written 8.6 years ago by • 0
0
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1
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1.4k
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Gene Symbol Annotation
medips
updated 8.6 years ago by ▴ 570 • written 8.6 years ago by • 0
0
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1
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1.3k
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TMM Normalization within MEDIPS ups some zero counts, is this normal?
MEDIPS
updated 8.7 years ago by ▴ 570 • written 8.7 years ago by • 0
1
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1
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1.8k
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MeDIPS and use of the 'bwa' parameter
R medip-seq medips bwa
updated 8.7 years ago by ▴ 570 • written 8.7 years ago by • 0
1
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6
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1.7k
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Alternative methylation contexts with MEDIPS?
MEDIPS
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by ▴ 90
0
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6
replies
2.0k
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MEDIPS - input
MEDIPS input
8.8 years ago GFM ▴ 20
0
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1
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1.4k
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Questions for MEDIPS getPairedGRange function in MEDIPS.readRegionsFile.R
medips bam file
8.8 years ago fkuo ▴ 10
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6
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2.4k
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MEDIPS: Number of windows tested in Paired-end data set
medips r
9.0 years ago peter.mcerlean • 0
0
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5
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2.0k
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MEDIPS genome Vs createROIset significance issue
medips r
9.1 years ago peter.mcerlean • 0
0
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1
reply
1.9k
views
Error in MEDIPS.calibrationCurve looking for different methylation profiles
medips R
updated 9.2 years ago by ▴ 570 • written 9.2 years ago by • 0
0
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1
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1.5k
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How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
R Medips edgeR
updated 9.2 years ago by ▴ 570 • written 9.2 years ago by • 0
50 results • Page 1 of 1
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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Thanks for your time on this, I have also never seen anything quite like this before neither. The only confounding variable I received in t…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.8k
If it was global changes then (in my head) why is there two populations of peaks (that to me indicates some sort of confouder) and also, if…
Comment: fast apply on RleList by story.benjamin ▴ 20
Here's a test data.set if you need: library(GenomicRanges) library(rtracklayer) # gr test test.gr <- GRanges(seqnames…
Answer: BiocParallel_1.40.1.tar.gz not available by shepherl 4.1k
Please try again. We have updated the BiocParallel package and BiocManager should work as expected (pulling 1.40.2 as source). The Landin…
Comment: BiocParallel_1.40.1.tar.gz not available by Johan • 0
Your approach works, but it implies manually rejecting the update of BiocParallel at each use of `BiocManager::install()`, which is pretty …
Votes
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
Comment: BiocParallel_1.40.1.tar.gz not available
Comment: BiocParallel_1.40.1.tar.gz not available
Limma outputs different results for same sample?
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