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qsea
•
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0
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249
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
8 months ago
User3088
• 0
0
votes
1
reply
609
views
QSEA:Error in h(simpleError(msg, call))
qsea
13 months ago
kf
• 0
1
vote
2
replies
635
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 17 months ago by
Researcher
▴ 10
0
votes
2
replies
722
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
20 months ago • updated 8 months ago
User3088
• 0
9
votes
18
replies
4.5k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 21 months ago by
Matthias Lienhard
▴ 280 • written 8.6 years ago by
justinburgener
▴ 20
2
votes
1
reply
877
views
QSEA: normalisation >> sequencing preference
qsea
updated 2.7 years ago by
Matthias Lienhard
▴ 280 • written 2.7 years ago by
a.riediger
▴ 20
1
vote
1
reply
1.3k
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 2.7 years ago by
Matthias Lienhard
▴ 280 • written 2.7 years ago by
a.riediger
▴ 20
1
vote
4
replies
1.8k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 3.1 years ago by
Simon Pearce
• 0 • written 3.1 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.3k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3.2 years ago by
Simon Pearce
• 0 • written 3.2 years ago by
Marianna
▴ 20
3
votes
8
replies
2.0k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
4.3 years ago
rtrivedi1
▴ 10
7
votes
9
replies
2.5k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
4.4 years ago
rtrivedi1
▴ 10
0
votes
1
reply
1.0k
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 4.4 years ago by
Matthias Lienhard
▴ 280 • written 4.6 years ago by
el466
• 0
1
vote
1
reply
1.4k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 4.8 years ago by
Matthias Lienhard
▴ 280 • written 4.8 years ago by
mbk0asis
• 0
0
votes
2
replies
1.1k
views
Qsea - plotCoverage
Qsea
updated 5.5 years ago by
Matthias Lienhard
▴ 280 • written 5.5 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.5k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 5.7 years ago by
Matthias Lienhard
▴ 280 • written 5.7 years ago by
Simon Pearce
• 0
0
votes
1
reply
1.0k
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 5.7 years ago by
Matthias Lienhard
▴ 280 • written 5.7 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
2.1k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 9 months ago by
Lukas
▴ 20 • written 6.2 years ago by
LNathanson
• 0
0
votes
0
replies
1.4k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
7.0 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 7.4 years ago by
Matthias Lienhard
▴ 280 • written 7.4 years ago by
apt.university
• 0
0
votes
8
replies
2.2k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 7.5 years ago by
Matthias Lienhard
▴ 280 • written 7.5 years ago by
wildist
• 0
0
votes
3
replies
1.6k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
geekyvt
• 0
1
vote
2
replies
1.4k
views
QSEA: Error while addLibraryFactors
QSEA
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
geekyvt
• 0
1
vote
3
replies
1.7k
views
QSEA Error while loading the bam files
qsea
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
geekyvt
• 0
23 results • Page
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Comment: DESeq2 for candidate gene analysis
by
horrible.junglefowl.xkxi
• 0
The free online calculator has become an indispensable tool in our digital world. Its versatility, accessibility, and ease of use make it a…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
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