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Qsea
•
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0
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0
replies
114
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
9 weeks ago
User3088
• 0
0
votes
1
reply
478
views
QSEA:Error in h(simpleError(msg, call))
qsea
6 months ago
kf
• 0
1
vote
2
replies
481
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 10 months ago by
Researcher
▴ 10
0
votes
2
replies
561
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
14 months ago • updated 9 weeks ago
User3088
• 0
9
votes
18
replies
4.0k
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 8.0 years ago by
justinburgener
▴ 20
2
votes
1
reply
754
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 2.6 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 2.7 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
3.9 years ago • updated 3.8 years ago
rtrivedi1
▴ 10
0
votes
1
reply
882
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 5.1 years ago by
Matthias Lienhard
▴ 280 • written 5.1 years ago by
Simon Pearce
• 0
0
votes
1
reply
910
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 12 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
6.5 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 6.9 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: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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