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qsea
•
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0
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285
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
10 months ago
User3088
• 0
0
votes
1
reply
645
views
QSEA:Error in h(simpleError(msg, call))
qsea
14 months ago
kf
• 0
1
vote
2
replies
664
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 19 months ago by
Researcher
▴ 10
0
votes
2
replies
752
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
22 months ago • updated 10 months ago
User3088
• 0
9
votes
18
replies
4.7k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 23 months ago by
Matthias Lienhard
▴ 280 • written 8.7 years ago by
justinburgener
▴ 20
2
votes
1
reply
915
views
QSEA: normalisation >> sequencing preference
qsea
updated 2.8 years ago by
Matthias Lienhard
▴ 280 • written 2.8 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 2.8 years ago by
Matthias Lienhard
▴ 280 • written 2.8 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 3.2 years ago by
Simon Pearce
• 0 • written 3.2 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.4k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3.3 years ago by
Simon Pearce
• 0 • written 3.4 years ago by
Marianna
▴ 20
3
votes
8
replies
2.1k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
4.5 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
4.6 years ago • updated 4.5 years ago
rtrivedi1
▴ 10
0
votes
1
reply
1.1k
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 4.6 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 5.8 years ago by
Matthias Lienhard
▴ 280 • written 5.8 years ago by
Simon Pearce
• 0
0
votes
1
reply
1.1k
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 5.8 years ago by
Matthias Lienhard
▴ 280 • written 5.8 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 6.3 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 7.5 years ago by
Matthias Lienhard
▴ 280 • written 7.5 years ago by
apt.university
• 0
0
votes
8
replies
2.3k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 7.6 years ago by
Matthias Lienhard
▴ 280 • written 7.6 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 7.8 years ago by
Matthias Lienhard
▴ 280 • written 7.8 years ago by
geekyvt
• 0
1
vote
2
replies
1.4k
views
QSEA: Error while addLibraryFactors
QSEA
updated 7.8 years ago by
Matthias Lienhard
▴ 280 • written 7.8 years ago by
geekyvt
• 0
1
vote
3
replies
1.7k
views
QSEA Error while loading the bam files
qsea
updated 7.8 years ago by
Matthias Lienhard
▴ 280 • written 7.8 years ago by
geekyvt
• 0
23 results • Page
1 of 1
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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