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Qsea
•
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0
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0
replies
127
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
12 weeks ago
User3088
• 0
0
votes
1
reply
501
views
QSEA:Error in h(simpleError(msg, call))
qsea
7 months ago
kf
• 0
1
vote
2
replies
502
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 11 months ago by
Researcher
▴ 10
0
votes
2
replies
575
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
14 months ago • updated 12 weeks ago
User3088
• 0
9
votes
18
replies
4.1k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 15 months ago by
Matthias Lienhard
▴ 280 • written 8.1 years ago by
justinburgener
▴ 20
2
votes
1
reply
766
views
QSEA: normalisation >> sequencing preference
qsea
updated 2.2 years ago by
Matthias Lienhard
▴ 280 • written 2.2 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 2.2 years ago by
Matthias Lienhard
▴ 280 • written 2.2 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 2.6 years ago by
Simon Pearce
• 0 • written 2.6 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.2k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 2.7 years ago by
Simon Pearce
• 0 • written 2.7 years ago by
Marianna
▴ 20
3
votes
8
replies
1.9k
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
3.9 years ago
rtrivedi1
▴ 10
0
votes
1
reply
894
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 3.9 years ago by
Matthias Lienhard
▴ 280 • written 4.1 years ago by
el466
• 0
1
vote
1
reply
1.3k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 4.3 years ago by
Matthias Lienhard
▴ 280 • written 4.3 years ago by
mbk0asis
• 0
0
votes
2
replies
1.0k
views
Qsea - plotCoverage
Qsea
updated 5.0 years ago by
Matthias Lienhard
▴ 280 • written 5.0 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.3k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 5.2 years ago by
Matthias Lienhard
▴ 280 • written 5.2 years ago by
Simon Pearce
• 0
0
votes
1
reply
923
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 5.2 years ago by
Matthias Lienhard
▴ 280 • written 5.2 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
2.0k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 3 months ago by
Lukas
▴ 20 • written 5.7 years ago by
LNathanson
• 0
0
votes
0
replies
1.3k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
6.5 years ago
saripalligautam86
▴ 10
0
votes
1
reply
1.1k
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 6.9 years ago by
Matthias Lienhard
▴ 280 • written 6.9 years ago by
apt.university
• 0
0
votes
8
replies
2.0k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 7.0 years ago by
Matthias Lienhard
▴ 280 • written 7.0 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 7.2 years ago by
Matthias Lienhard
▴ 280 • written 7.2 years ago by
geekyvt
• 0
1
vote
2
replies
1.3k
views
QSEA: Error while addLibraryFactors
QSEA
updated 7.2 years ago by
Matthias Lienhard
▴ 280 • written 7.2 years ago by
geekyvt
• 0
1
vote
3
replies
1.6k
views
QSEA Error while loading the bam files
qsea
updated 7.2 years ago by
Matthias Lienhard
▴ 280 • written 7.2 years ago by
geekyvt
• 0
23 results • Page
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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