User: Lescai, Francesco
Lescai, Francesco • 380
- Reputation:
- 380
- Status:
- Trusted
- Location:
- Denmark
- Last seen:
- 7 months, 1 week ago
- Joined:
- 5 years, 11 months ago
- Email:
- l*****@biomed.au.dk
Posts by Lescai, Francesco
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... Hi Michael,
I've updated also R to 3.5.1 now and it does work. and ggbio is now 1.28.5
the vignette is now updated to
circle(hg19sub, geom = "text", aes(label = seqnames), vjust = 0, size = 3)
instead of
circle(hg19sub, geom = "text", aes(label = seqnames(hg19sub)), vjust = -1.5, size = 3)
mig ...
written 7 months ago by
Lescai, Francesco • 380
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... Hi guys,
I'm following the vignette to create a circular plot
ggbio()+
circle(myGR, geom = "link", linked.to = "toRegion", aes(color = dataset))+
circle(hg19IdeogramCyto, geom = "ideo", fill = "gray70") +
circle(hg19IdeogramCyto, geom = "scale", size = 2) +
circle(hg19IdeogramCyto, geom = ...
written 7 months ago by
Lescai, Francesco • 380
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376
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... .Rmd with RStudio, using knitR
...
written 18 months ago by
Lescai, Francesco • 380
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376
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... Hi guys,
I've searched for this without success and maybe there's a banal solution :) how do I keep in place a figure when I'm using BiocStyle to output a PDF? seems the default is floating, but couldn't find a way to change it.
Sometimes I find it useful to have the figure right before or after t ...
written 18 months ago by
Lescai, Francesco • 380
• updated
18 months ago by
Andrzej Oleś • 720
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... I sent one of my fast5 to Mike via email. I suppose they're working on it. Looking fwd to hear something too.
...
written 19 months ago by
Lescai, Francesco • 380
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... Hi there,
I have now a similar problem related to HDF5 reading.
We sequenced with Nanopore last week and although I tried to update all packages, I get this error message
```
> library(IONiseR)
> fast5files <- list.files(path = "/data/nanopore/nano_20170831/fast5/pass/0/", pattern = ".fa ...
written 19 months ago by
Lescai, Francesco • 380
0
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1
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617
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1
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... Hi there,
I do apologise if this question has been posted already: I am plotting some gene tracks with ggbio/autoplot and would like to plot genes (not transcripts, or collapsing the transcripts into genes), but I'd like to have close/overlapping genes not plotted on top of each other.
the code is ...
written 2.9 years ago by
Lescai, Francesco • 380
• updated
2.9 years ago by
James W. MacDonald ♦ 49k
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... I also tried to use a more updated version, but the error is the same
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB ...
written 3.1 years ago by
Lescai, Francesco • 380
0
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4
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1.4k
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4
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... Hi Valerie,
I seem to have the same problem (it's a very large VCF file, with 4,500 samples), but I am indeed subsetting the file.
I compressed it and tabix'ed it. and I'm requesting
fl <- "exome.recalibrated.vcf.gz"
hdr <- scanVcfHeader(fl)
vcf <- readVcf(fl, genome="hg38", param=ScanVcfP ...
written 3.1 years ago by
Lescai, Francesco • 380
0
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3
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692
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3
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Answer:
A: ontoCAT getEFO error
... yep, and I can confirm is the combination of ontoCAT 20 + R 3.2
with this, it works.
thanks
> library(ontoCAT)
Loading required package: rJava
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)
locale:
[1] en_GB.U ...
written 4.0 years ago by
Lescai, Francesco • 380
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