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qsea
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0
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276
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Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
9 months ago
User3088
• 0
0
votes
1
reply
633
views
QSEA:Error in h(simpleError(msg, call))
qsea
14 months ago
kf
• 0
1
vote
2
replies
650
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 18 months ago by
Researcher
▴ 10
0
votes
2
replies
741
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
21 months ago • updated 9 months ago
User3088
• 0
9
votes
18
replies
4.6k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 22 months ago by
Matthias Lienhard
▴ 280 • written 8.6 years ago by
justinburgener
▴ 20
2
votes
1
reply
899
views
QSEA: normalisation >> sequencing preference
qsea
updated 2.7 years ago by
Matthias Lienhard
▴ 280 • written 2.7 years ago by
a.riediger
▴ 20
1
vote
1
reply
1.3k
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 2.7 years ago by
Matthias Lienhard
▴ 280 • written 2.7 years ago by
a.riediger
▴ 20
1
vote
4
replies
1.9k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 3.1 years ago by
Simon Pearce
• 0 • written 3.2 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.3k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3.3 years ago by
Simon Pearce
• 0 • written 3.3 years ago by
Marianna
▴ 20
3
votes
8
replies
2.1k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
4.4 years ago
rtrivedi1
▴ 10
7
votes
9
replies
2.6k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
4.5 years ago
rtrivedi1
▴ 10
0
votes
1
reply
1.0k
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 4.5 years ago by
Matthias Lienhard
▴ 280 • written 4.7 years ago by
el466
• 0
1
vote
1
reply
1.4k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 4.9 years ago by
Matthias Lienhard
▴ 280 • written 4.9 years ago by
mbk0asis
• 0
0
votes
2
replies
1.2k
views
Qsea - plotCoverage
Qsea
updated 5.6 years ago by
Matthias Lienhard
▴ 280 • written 5.6 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.6k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 5.7 years ago by
Matthias Lienhard
▴ 280 • written 5.7 years ago by
Simon Pearce
• 0
0
votes
1
reply
1.1k
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 5.7 years ago by
Matthias Lienhard
▴ 280 • written 5.7 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
2.2k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 10 months ago by
Lukas
▴ 20 • written 6.2 years ago by
LNathanson
• 0
0
votes
0
replies
1.5k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
7.1 years ago
saripalligautam86
▴ 10
0
votes
1
reply
1.2k
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 7.4 years ago by
Matthias Lienhard
▴ 280 • written 7.5 years ago by
apt.university
• 0
0
votes
8
replies
2.2k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 7.5 years ago by
Matthias Lienhard
▴ 280 • written 7.5 years ago by
wildist
• 0
0
votes
3
replies
1.7k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
geekyvt
• 0
1
vote
2
replies
1.4k
views
QSEA: Error while addLibraryFactors
QSEA
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
geekyvt
• 0
1
vote
3
replies
1.7k
views
QSEA Error while loading the bam files
qsea
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
geekyvt
• 0
23 results • Page
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Comment: Getting a large intercept with DESeq2
by
Michael Love
43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
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by
James W. MacDonald
68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2
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The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
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There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
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Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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