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QSEA
•
reset
7
votes
9
replies
1.7k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
3.0 years ago • updated 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 4 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
2.9 years ago
rtrivedi1
▴ 10
2
votes
1
reply
497
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
950
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
623
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
1.0k
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
767
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
642
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 3.0 years ago by
Matthias Lienhard
▴ 240 • written 3.1 years ago by
el466
• 0
0
votes
1
reply
176
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 6 weeks ago by
Simon Pearce
• 0 • written 12 weeks ago by
User3088
• 0
0
votes
2
replies
835
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 21 months ago by
Simon Pearce
• 0 • written 21 months ago by
Marianna
▴ 20
0
votes
1
reply
854
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
863
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
987
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
5.6 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
684
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
1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Votes
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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