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Qsea
•
reset
3
votes
8
replies
473
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
11 months ago
rtrivedi1
▴ 10
7
votes
9
replies
698
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
12 months ago • updated 11 months ago
rtrivedi1
▴ 10
0
votes
1
reply
247
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 12 months ago by
Matthias Lienhard
▴ 220 • written 14 months ago by
el466
• 0
0
votes
1
reply
349
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 16 months ago by
Matthias Lienhard
▴ 220 • written 16 months ago by
mbk0asis
• 0
0
votes
2
replies
276
views
Qsea - plotCoverage
Qsea
updated 2.1 years ago by
Matthias Lienhard
▴ 220 • written 2.1 years ago by
gaurav4thareja
▴ 20
0
votes
2
replies
329
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 2.2 years ago by
Matthias Lienhard
▴ 220 • written 2.2 years ago by
Simon Pearce
• 0
0
votes
1
reply
268
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 2.2 years ago by
Matthias Lienhard
▴ 220 • written 2.2 years ago by
gaurav4thareja
▴ 20
0
votes
2
replies
412
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 2.7 years ago by
Matthias Lienhard
▴ 220 • written 2.8 years ago by
LNathanson
• 0
0
votes
0
replies
438
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
3.6 years ago
saripalligautam86
▴ 10
0
votes
1
reply
458
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 3.9 years ago by
Matthias Lienhard
▴ 220 • written 4.0 years ago by
apt.university
• 0
0
votes
8
replies
872
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 4.0 years ago by
Matthias Lienhard
▴ 220 • written 4.1 years ago by
wildist
• 0
0
votes
3
replies
637
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 4.3 years ago by
Matthias Lienhard
▴ 220 • written 4.3 years ago by
geekyvt
• 0
1
vote
2
replies
541
views
QSEA: Error while addLibraryFactors
QSEA
updated 4.3 years ago by
Matthias Lienhard
▴ 220 • written 4.3 years ago by
geekyvt
• 0
1
vote
3
replies
780
views
QSEA Error while loading the bam files
qsea
updated 4.3 years ago by
Matthias Lienhard
▴ 220 • written 4.3 years ago by
geekyvt
• 0
7
votes
17
replies
1.5k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 21 months ago by
Matthias Lienhard
▴ 220 • written 5.1 years ago by
justinburgener
▴ 20
15 results • Page
1 of 1
Recent ...
Replies
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Hi Michael, I performed Differential isoform expression analysis using Swish and have got some isoforms. I had previously performed the g…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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