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OmicCircos
•
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0
votes
0
replies
520
views
Question about OmicCircos
OmicCircos
5.4 years ago
ch8316f5eyu
• 0
0
votes
0
replies
767
views
Synteny plots with OmicCircos or Rcircos
omiccircos
rcircos
6.0 years ago
mictadlo
▴ 10
0
votes
0
replies
772
views
Omiccircos: how to draw a circos plot for non-model organisms
omiccircos
seganglepo
sim.circos
circos
6.1 years ago
Didi
▴ 10
2
votes
3
replies
3.2k
views
Making a circos plot to show expression for a gene set rather than whole genome
Gene set
gene set analysis
omiccircos
updated 6.1 years ago by
yifangt
▴ 20 • written 8.7 years ago by
Peter.Wood
• 0
0
votes
0
replies
1.1k
views
OmicCircos: included UCSC.hg19.chr dataframe is actually hg18 cytobands
omiccircos
bug
hg19
hg18
data
6.4 years ago
matthew.bashton
• 0
0
votes
1
reply
1.4k
views
Circos Tile colors
OmicCircos
RCircos
updated 6.4 years ago by
bernatgel
▴ 150 • written 6.4 years ago by
Radek
▴ 90
0
votes
1
reply
2.1k
views
OmicCircos - Error in 1:scale.n : NA/NaN argument
OmicCircos
6.5 years ago
Stefan Langenberg
• 0
0
votes
0
replies
1.0k
views
OmicCircos Error in Colnames attribute mus be the same length as the vector
r
omiccircos
6.7 years ago
theobroma22
▴ 10
0
votes
0
replies
1.1k
views
OmicCircos barplot height and scale
omiccircos
6.7 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
0
votes
0
replies
644
views
OmicCircos for non human genomes
omiccircos
rnaseq
plants
6.7 years ago
Didi
▴ 10
0
votes
0
replies
740
views
Zoom function in OmicCircos
OmicCircos
Zoom
6.7 years ago
abmora
• 0
0
votes
0
replies
668
views
How to plot a single segment using OmicCircos?
omiccircos
7.1 years ago
Shambho
• 0
1
vote
0
replies
663
views
the 23re and 24th segs cannot be plotted
OmicCircos
7.3 years ago
magcj89
▴ 10
3
votes
2
replies
2.3k
views
How to represent a relationship between physical map and linkage map of a sequenced data using OmicCircos or another similar
omiccircos
software R
bioconductor for genomic data science
linkage disequilibrium
updated 7.5 years ago by
Hu, Ying NIH/NCI [E]
▴ 50 • written 7.5 years ago by
pertille
• 0
0
votes
0
replies
1.1k
views
Can OmicCircos handle chicken ChIA-PET interactome?
OmicCircos
chicken
7.7 years ago
Gary
▴ 20
0
votes
0
replies
1.2k
views
Circos Styling plots is now easy with canceR package
canceR
visualization
omiccircos
8.4 years ago
kmezhoud
▴ 10
0
votes
0
replies
1.2k
views
News:
OmicCircos was updated
visualization
omiccircos
News
8.5 years ago
Hu, Ying NIH/NCI [E]
▴ 50
1
vote
3
replies
1.4k
views
OmicCircos mapping data file.
omiccircos
updated 8.5 years ago by
Hu, Ying NIH/NCI [E]
▴ 50 • written 8.9 years ago by
abdul rawoof
▴ 60
0
votes
1
reply
1.6k
views
extdata missing for non-human OmicCircos plots?
OmicCircos
updated 8.5 years ago by
Hu, Ying NIH/NCI [E]
▴ 50 • written 8.9 years ago by
micahgearhart
• 0
0
votes
2
replies
1.7k
views
How to specifiy colors for polygon links when using circos function of OmicCircos package
graph
omiccircos
updated 8.6 years ago by
Hu, Ying NIH/NCI [E]
▴ 50 • written 8.6 years ago by
wei.shen
• 0
0
votes
1
reply
1.2k
views
Larger values masking others for OmicCircos heatmap
differential gene expression
heatmap
Circos
omiccircos
8.7 years ago
Peter.Wood
• 0
21 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.
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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.…
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by
ATpoint
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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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