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segmentation
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316
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Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM
Segmentation
CINdex
VCF
Data
13 months ago
raven1306
• 0
0
votes
1
reply
568
views
PureCN: Why is average coverage used for segmentation and not the denoised fragment counts?
PureCN
CNV
CNA
segmentation
calculateTangentNormal
updated 3.8 years ago by
markus.riester
▴ 130 • written 3.8 years ago by
sruddy17
• 0
0
votes
0
replies
628
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation
reference
CNA
TCGA
4.6 years ago
jlarsen728
• 0
1
vote
5
replies
954
views
CRImage createTrainingSet package is not available to install
classification
segmentation
cell types
image analysis
crimage
5.1 years ago
Jenny.chien
• 0
0
votes
3
replies
1.3k
views
Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
TCGA
Cancer
dnacopy
segmentation
updated 6.2 years ago by
markus.riester
▴ 130 • written 6.2 years ago by
Luisa672
• 0
1
vote
2
replies
1.1k
views
DNAcopy segmentation issue: min.width argument not working?
dnacopy
segmentation
CBS
updated 6.6 years ago by
Venkat Seshan
▴ 30 • written 6.6 years ago by
W. C.
▴ 10
0
votes
2
replies
970
views
GCRMA segmentation fault
gcrma
segmentation
fault
segfault
updated 7.5 years ago by
James W. MacDonald
63k • written 7.5 years ago by
kazi
• 0
7 results • Page
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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta
by
Michael Love
40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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