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Qsea
•
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0
votes
1
reply
309
views
QSEA:Error in h(simpleError(msg, call))
qsea
10 weeks ago
kf
• 0
0
votes
2
replies
354
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 6 months ago by
Researcher
• 0
0
votes
1
reply
388
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 8 months ago by
Simon Pearce
• 0 • written 9 months ago by
User3088
• 0
9
votes
18
replies
3.7k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 11 months ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
justinburgener
▴ 20
2
votes
1
reply
669
views
QSEA: normalisation >> sequencing preference
qsea
updated 21 months ago by
Matthias Lienhard
▴ 280 • written 21 months ago by
a.riediger
▴ 20
1
vote
1
reply
929
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 21 months ago by
Matthias Lienhard
▴ 280 • written 21 months ago by
a.riediger
▴ 20
1
vote
4
replies
1.4k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 2.2 years ago by
Simon Pearce
• 0 • written 2.2 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.0k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 2.3 years ago by
Simon Pearce
• 0 • written 2.3 years ago by
Marianna
▴ 20
3
votes
8
replies
1.7k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
3.4 years ago
rtrivedi1
▴ 10
7
votes
9
replies
2.0k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
3.5 years ago
rtrivedi1
▴ 10
0
votes
1
reply
804
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 3.5 years ago by
Matthias Lienhard
▴ 280 • written 3.7 years ago by
el466
• 0
1
vote
1
reply
1.2k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 3.9 years ago by
Matthias Lienhard
▴ 280 • written 3.9 years ago by
mbk0asis
• 0
0
votes
2
replies
937
views
Qsea - plotCoverage
Qsea
updated 4.6 years ago by
Matthias Lienhard
▴ 280 • written 4.6 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.2k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 4.8 years ago by
Matthias Lienhard
▴ 280 • written 4.8 years ago by
Simon Pearce
• 0
0
votes
1
reply
837
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 4.8 years ago by
Matthias Lienhard
▴ 280 • written 4.8 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.4k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 5.3 years ago by
Matthias Lienhard
▴ 280 • written 5.3 years ago by
LNathanson
• 0
0
votes
0
replies
1.2k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
6.1 years ago
saripalligautam86
▴ 10
0
votes
1
reply
976
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 6.5 years ago by
Matthias Lienhard
▴ 280 • written 6.5 years ago by
apt.university
• 0
0
votes
8
replies
1.8k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 6.6 years ago by
Matthias Lienhard
▴ 280 • written 6.6 years ago by
wildist
• 0
0
votes
3
replies
1.4k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 6.8 years ago by
Matthias Lienhard
▴ 280 • written 6.8 years ago by
geekyvt
• 0
1
vote
2
replies
1.2k
views
QSEA: Error while addLibraryFactors
QSEA
updated 6.8 years ago by
Matthias Lienhard
▴ 280 • written 6.8 years ago by
geekyvt
• 0
1
vote
3
replies
1.5k
views
QSEA Error while loading the bam files
qsea
updated 6.8 years ago by
Matthias Lienhard
▴ 280 • written 6.8 years ago by
geekyvt
• 0
22 results • Page
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Comment: What type of counts data to import for performing Isoform analysis in edgeR
by
mohammedtoufiq91
▴ 10
@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…
Comment: athPkgBuilder data source :missing probesets
by
bobihanigujjar
• 0
In this article, we'll explore the demand for unbranded BJJ Gis and the benefits of choosing unbranded Gis for customization. [does anyone …
Comment: Crossover design with limma
by
SamGG
▴ 360
IMHO, here are the missing annotations treatmentdrug_orderDrugPlac - treatmentplacebo_orderDrugPlac, # effect of drug for the Drug…
Answer: What type of counts data to import for performing Isoform analysis in edgeR
by
ATpoint
★ 4.5k
You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…
Comment: makeContrastsDream for Interaction
by
abadgerw
• 0
Thank you! I will try this out.
Votes
Comment: ANOVA like approach of edgeR
Comment: Crossover design with limma
Answer: DESeq2 normalization vs VST vs rlog
Comment: makeContrastsDream for Interaction
Answer: Limma- Print-tip loess normalisation-printer layout information does not match M
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