User: Lescai, Francesco

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Posts by Lescai, Francesco

<prev • 44 results • page 1 of 5 • next >
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Comment: C: no floating figures with biocstyle
... .Rmd with RStudio, using knitR ...
written 11 days ago by Lescai, Francesco370
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no floating figures with biocstyle
... 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 ...
biocstyle float written 11 days ago by Lescai, Francesco370 • updated 10 days ago by Andrzej Oleś670
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Answer: A: Problem with readFast5Summary in IONiseR related to HDF5
... I sent one of my fast5 to Mike via email. I suppose they're working on it. Looking fwd to hear something too.   ...
written 5 weeks ago by Lescai, Francesco370
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Answer: A: Problem with readFast5Summary in IONiseR related to HDF5
... 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 6 weeks ago by Lescai, Francesco370
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ggbio OrganismDb autoplot - reduce vs identity
... 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 ...
ggbio autoplot written 17 months ago by Lescai, Francesco370 • updated 17 months ago by James W. MacDonald44k
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Answer: A: Error in reading 1000 genomes data
... 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 19 months ago by Lescai, Francesco370
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Answer: A: Error in reading 1000 genomes data
... 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 19 months ago by Lescai, Francesco370
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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 2.5 years ago by Lescai, Francesco370
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Answer: A: ontoCAT getEFO error
... Hi Natalja, thanks for your quick reply. I've updated it from source (the version I get from biocLite is the one related to my R version 3.1 and not 3.2) but it still doesn't work > sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) locale: [1] en_GB.UTF-8/ ...
written 2.5 years ago by Lescai, Francesco370
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ontoCAT getEFO error
... Hi guys, I’m trying to use the package ontoCAT but I keep having issues just starting up. I followed the vignettes and wasn’t able to load the EFO ontologies efo <- getEFO() Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl”. I checked on the website, an ...
ontocat ontologies efo written 2.5 years ago by Lescai, Francesco370

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Popular Question 13 months ago, created a question with more than 1,000 views. For getBM returns shorter vectors than values

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