User: Ugo Borello

gravatar for Ugo Borello
Ugo Borello340
Reputation:
340
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Location:
France
Last seen:
8 months, 1 week ago
Joined:
4 years, 9 months ago
Email:
u**********@inserm.fr

Posts by Ugo Borello

<prev • 38 results • page 1 of 4 • next >
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Answer: A: organism name error with makeTxDbPackageFromUCSC()
... Thank you very very much! Ugo ...
written 9 months ago by Ugo Borello340
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organism name error with makeTxDbPackageFromUCSC()
... Dear All, I am trying to make a TxDb package from the UCSC Macaca fascicularis annotation. I run: makeTxDbPackageFromUCSC( version="0.1", maintainer="UB", author="UB", destDir="/Library/Frameworks/R.framework/Versions/3.3/Resources/library", license="Artistic-2.0", genome="macFas5", ...
genomicfeatures maketxdbpackagefromucsc written 9 months ago by Ugo Borello340
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Answer: A: systemPipeR with DESeq2
... I will try, thank you Ugo   ...
written 3.1 years ago by Ugo Borello340
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Answer: A: systemPipeR with DESeq2
... Thank you, Thomas, for your reply.   And what about the filterDEGs() function, could I use it with the results obtained with DESeq2 and then take advantage of the systemPipeR workflow for downstream GO analysis?   Ugo ...
written 3.1 years ago by Ugo Borello340
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systemPipeR with DESeq2
... Dear Thomas, I was wondering if there is an easy way of using systemPipeR with DESeq2. Thank you   Ugo ...
deseq2 systempiper written 3.1 years ago by Ugo Borello340
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Comment: C: ChiPQC and paired-end data
... Thank you Thomas, > You could use paired-end data with ChIPQC but for now this would require you > to filter your Bam file for only "first read in pair" in order to avoid double > counting and biasing the cross-coverage scores plots. > This should be pretty straightforward to do using s ...
written 3.3 years ago by Ugo Borello340
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Comment: C: NCBI gff3 annotation file and read.gff()
... Thank you very much Michael and Martin, it worked. Ugo From: Michael Lawrence Date: Wed, 16 Jul 2014 05:35:19 -0700 To: Ugo Borello Cc: "bioconductor@r-project.org" Subject: Re: [BioC] NCBI gff3 annotation file and read.gff() Takes a couple of minutes but seems to work with: gff <- rtra ...
written 3.4 years ago by Ugo Borello340
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ChiPQC and paired-end data
... Dear Rory, I have few basic questions about ChiPQC. - Could I use ChiPQC with paired-end data? - I would like to use my mouse blacklist https://sites.google.com/site/anshulkundaje/projects/blacklists MOUSE (mm9): http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-bla cklist .bed.g ...
chipqc written 3.4 years ago by Ugo Borello340 • updated 3.3 years ago by Carroll, Thomas20
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NCBI gff3 annotation file and read.gff()
... Hi, I am trying to read without success, a gff file downloaded from the NCBI genomes ftp directory. library("genomes") > annot <- read.gff('~/Desktop/NCBI_Anno/ref_Macaca_fascicularis_5.0_top_level.gf f3') Error in `$<-.data.frame`(`*tmp*`, "description", value = "") : replacement has 1 ...
written 3.4 years ago by Ugo Borello340 • updated 3.4 years ago by Martin Morgan ♦♦ 20k
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Comment: C: NCBI gff3 annotation file and read.gff()
... Yes, indeed, I would like to mine into the fascicularis transcriptome and using makeTranscriptDbFromGFF() with my gff file is a very good suggestion. I tried earlier this approach but I have to confess that I was unable to specify an exonRankAttributeName value. I shall try to figure it out more car ...
written 3.4 years ago by Ugo Borello340

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Popular Question 8 months ago, created a question with more than 1,000 views. For DESeq2 multifactorial formula
Popular Question 2.8 years ago, created a question with more than 1,000 views. For DESeq2 multifactorial formula

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