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qsea
•
reset
7
votes
9
replies
1.6k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
2.9 years ago
rtrivedi1
▴ 10
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 3 months ago by
Matthias Lienhard
▴ 240 • written 7.1 years ago by
justinburgener
▴ 20
3
votes
8
replies
1.4k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
2.8 years ago
rtrivedi1
▴ 10
2
votes
1
reply
487
views
QSEA: normalisation >> sequencing preference
qsea
updated 14 months ago by
Matthias Lienhard
▴ 240 • written 14 months ago by
a.riediger
▴ 20
1
vote
2
replies
934
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 4.2 years ago by
Matthias Lienhard
▴ 240 • written 4.2 years ago by
Simon Pearce
• 0
1
vote
1
reply
605
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 14 months ago by
Matthias Lienhard
▴ 240 • written 14 months ago by
a.riediger
▴ 20
1
vote
4
replies
1.1k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 19 months ago by
Simon Pearce
• 0 • written 19 months ago by
a.riediger
▴ 20
1
vote
2
replies
995
views
QSEA: Error while addLibraryFactors
QSEA
updated 6.2 years ago by
Matthias Lienhard
▴ 240 • written 6.2 years ago by
geekyvt
• 0
1
vote
3
replies
1.3k
views
QSEA Error while loading the bam files
qsea
updated 6.2 years ago by
Matthias Lienhard
▴ 240 • written 6.2 years ago by
geekyvt
• 0
0
votes
2
replies
762
views
Qsea - plotCoverage
Qsea
updated 4.0 years ago by
Matthias Lienhard
▴ 240 • written 4.0 years ago by
gaurav4thareja
▴ 20
0
votes
3
replies
1.2k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 6.2 years ago by
Matthias Lienhard
▴ 240 • written 6.2 years ago by
geekyvt
• 0
0
votes
1
reply
636
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 2.9 years ago by
Matthias Lienhard
▴ 240 • written 3.1 years ago by
el466
• 0
0
votes
1
reply
168
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 5 weeks ago by
Simon Pearce
• 0 • written 11 weeks ago by
User3088
• 0
0
votes
2
replies
827
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 20 months ago by
Simon Pearce
• 0 • written 21 months ago by
Marianna
▴ 20
0
votes
1
reply
846
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 3.3 years ago by
Matthias Lienhard
▴ 240 • written 3.3 years ago by
mbk0asis
• 0
0
votes
8
replies
1.6k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 6.0 years ago by
Matthias Lienhard
▴ 240 • written 6.0 years ago by
wildist
• 0
0
votes
1
reply
854
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 5.9 years ago by
Matthias Lienhard
▴ 240 • written 5.9 years ago by
apt.university
• 0
0
votes
0
replies
979
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
5.5 years ago
saripalligautam86
▴ 10
0
votes
2
replies
1.1k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 4.7 years ago by
Matthias Lienhard
▴ 240 • written 4.7 years ago by
LNathanson
• 0
0
votes
1
reply
676
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 4.2 years ago by
Matthias Lienhard
▴ 240 • written 4.2 years ago by
gaurav4thareja
▴ 20
20 results • Page
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Replies
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Answer: List of Deprecated Packages for Bioc3.19
by
shepherl
3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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