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QSEA
•
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0
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0
replies
108
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
7 weeks ago
User3088
• 0
0
votes
1
reply
461
views
QSEA:Error in h(simpleError(msg, call))
qsea
6 months ago
kf
• 0
1
vote
2
replies
468
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 10 months ago by
Researcher
▴ 10
0
votes
2
replies
551
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
13 months ago • updated 7 weeks ago
User3088
• 0
9
votes
18
replies
3.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 14 months ago by
Matthias Lienhard
▴ 280 • written 8.0 years ago by
justinburgener
▴ 20
2
votes
1
reply
750
views
QSEA: normalisation >> sequencing preference
qsea
updated 2.1 years ago by
Matthias Lienhard
▴ 280 • written 2.1 years ago by
a.riediger
▴ 20
1
vote
1
reply
1.1k
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 2.1 years ago by
Matthias Lienhard
▴ 280 • written 2.1 years ago by
a.riediger
▴ 20
1
vote
4
replies
1.6k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 2.5 years ago by
Simon Pearce
• 0 • written 2.5 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.1k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 2.6 years ago by
Simon Pearce
• 0 • written 2.6 years ago by
Marianna
▴ 20
3
votes
8
replies
1.8k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
3.8 years ago
rtrivedi1
▴ 10
7
votes
9
replies
2.2k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
3.8 years ago
rtrivedi1
▴ 10
0
votes
1
reply
875
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 3.8 years ago by
Matthias Lienhard
▴ 280 • written 4.0 years ago by
el466
• 0
1
vote
1
reply
1.3k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 4.2 years ago by
Matthias Lienhard
▴ 280 • written 4.2 years ago by
mbk0asis
• 0
0
votes
2
replies
998
views
Qsea - plotCoverage
Qsea
updated 4.9 years ago by
Matthias Lienhard
▴ 280 • written 4.9 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.3k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 5.1 years ago by
Matthias Lienhard
▴ 280 • written 5.1 years ago by
Simon Pearce
• 0
0
votes
1
reply
903
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 5.1 years ago by
Matthias Lienhard
▴ 280 • written 5.1 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
1.9k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 10 weeks ago by
Lukas
▴ 20 • written 5.6 years ago by
LNathanson
• 0
0
votes
0
replies
1.3k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
6.4 years ago
saripalligautam86
▴ 10
0
votes
1
reply
1.0k
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 6.8 years ago by
Matthias Lienhard
▴ 280 • written 6.8 years ago by
apt.university
• 0
0
votes
8
replies
2.0k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 6.9 years ago by
Matthias Lienhard
▴ 280 • written 6.9 years ago by
wildist
• 0
0
votes
3
replies
1.5k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 7.1 years ago by
Matthias Lienhard
▴ 280 • written 7.1 years ago by
geekyvt
• 0
1
vote
2
replies
1.3k
views
QSEA: Error while addLibraryFactors
QSEA
updated 7.1 years ago by
Matthias Lienhard
▴ 280 • written 7.1 years ago by
geekyvt
• 0
1
vote
3
replies
1.6k
views
QSEA Error while loading the bam files
qsea
updated 7.1 years ago by
Matthias Lienhard
▴ 280 • written 7.1 years ago by
geekyvt
• 0
23 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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