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qsea
•
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0
votes
1
reply
385
views
QSEA:Error in h(simpleError(msg, call))
qsea
4 months ago
kf
• 0
1
vote
2
replies
403
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 8 months ago by
Researcher
▴ 10
0
votes
1
reply
421
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 10 months ago by
Simon Pearce
• 0 • written 11 months ago by
User3088
• 0
9
votes
18
replies
3.8k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 12 months ago by
Matthias Lienhard
▴ 280 • written 7.8 years ago by
justinburgener
▴ 20
2
votes
1
reply
699
views
QSEA: normalisation >> sequencing preference
qsea
updated 23 months ago by
Matthias Lienhard
▴ 280 • written 23 months ago by
a.riediger
▴ 20
1
vote
1
reply
985
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 23 months ago by
Matthias Lienhard
▴ 280 • written 23 months ago by
a.riediger
▴ 20
1
vote
4
replies
1.5k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 2.3 years ago by
Simon Pearce
• 0 • written 2.4 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.1k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 2.5 years ago by
Simon Pearce
• 0 • written 2.5 years ago by
Marianna
▴ 20
3
votes
8
replies
1.8k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
3.6 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
3.7 years ago • updated 3.6 years ago
rtrivedi1
▴ 10
0
votes
1
reply
830
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 3.7 years ago by
Matthias Lienhard
▴ 280 • written 3.9 years ago by
el466
• 0
1
vote
1
reply
1.2k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 4.1 years ago by
Matthias Lienhard
▴ 280 • written 4.1 years ago by
mbk0asis
• 0
0
votes
2
replies
958
views
Qsea - plotCoverage
Qsea
updated 4.8 years ago by
Matthias Lienhard
▴ 280 • written 4.8 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.3k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 4.9 years ago by
Matthias Lienhard
▴ 280 • written 4.9 years ago by
Simon Pearce
• 0
0
votes
1
reply
862
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 4.9 years ago by
Matthias Lienhard
▴ 280 • written 4.9 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
1.8k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 13 days ago by
Lukas
▴ 20 • written 5.4 years ago by
LNathanson
• 0
0
votes
0
replies
1.2k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
6.3 years ago
saripalligautam86
▴ 10
0
votes
1
reply
998
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 6.6 years ago by
Matthias Lienhard
▴ 280 • written 6.7 years ago by
apt.university
• 0
0
votes
8
replies
1.9k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 6.7 years ago by
Matthias Lienhard
▴ 280 • written 6.7 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 6.9 years ago by
Matthias Lienhard
▴ 280 • written 6.9 years ago by
geekyvt
• 0
1
vote
2
replies
1.2k
views
QSEA: Error while addLibraryFactors
QSEA
updated 6.9 years ago by
Matthias Lienhard
▴ 280 • written 6.9 years ago by
geekyvt
• 0
1
vote
3
replies
1.5k
views
QSEA Error while loading the bam files
qsea
updated 6.9 years ago by
Matthias Lienhard
▴ 280 • written 6.9 years ago by
geekyvt
• 0
22 results • Page
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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2
by
James W. MacDonald
67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Blandine
• 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
James W. MacDonald
67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data
by
Leonardo Collado Torres
★ 1.1k
Thanks @fep29! ^^
Votes
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
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