User: Charles Plessy

gravatar for Charles Plessy
Charles Plessy1.5k
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Japan
Website:
http://population-tran...
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2 hours ago
Joined:
2 years, 7 months ago
Email:
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Posts by Charles Plessy

<prev • 174 results • page 1 of 18 • next >
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Answer: A: What should we consider when setting up a bioinformatics web service?
... Be clear to yourself and the users on how long the web service will be supported before its discontinuation will be on the agenda. Major events leading to predictable discontinuation include: - non-renewal of the research laboratory when it it subjected to periodic evaluation, - end of funding, ...
written 1 day ago by Charles Plessy1.5k
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Comment: C: CAGE seq & RNA-seq
... Then you may be quite interested in the [expression atlas](http://fantom.gsc.riken.jp/cat/?fd=expression%2Fexpression_atlas) of the FANTOM CAGE associated transcriptome ([FANTOM CAT](http://fantom.gsc.riken.jp/cat/)). ...
written 3 days ago by Charles Plessy1.5k
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Answer: A: CAGE seq & RNA-seq
... To take the best from a [CAGE](https://en.wikipedia.org/wiki/Cap_analysis_gene_expression) experiment, I recommend to call peaks from the 5′ ends of the aligned CAGE reads (for instance with [paraclu](http://cbrc3.cbrc.jp/~martin/paraclu/), and run the differential expression analysis at the peak le ...
written 3 days ago by Charles Plessy1.5k
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Answer: A: How do I get the promoter region of mammalian lncRNAs?
... Freshly published: [An atlas of human long non-coding RNAs with accurate 5’ ends](http://fantom.gsc.riken.jp/cat/), from my colleague Chung and many others. ...
written 11 days ago by Charles Plessy1.5k
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... I think that you have to learn about *design formula* and *design matrices*, that DESseq2 and other packages use to describe experimental designs like yours. The topic is covered in the DESeq2 manual and many posts on the Bioconductor support forum, and is a bit too complex for me to introduce it br ...
written 11 days ago by Charles Plessy1.5k
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Comment: C: Looking for an open-source programmer, Yokohama, Japan
... Yes, the call is still open! ...
written 11 days ago by Charles Plessy1.5k
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Answer: A: Which avenue is appropriate for submitting publication based on novel bioconduct
... > From my point of view, submitting my packages to Bioinformatics could be risky I am not sure what you mean by *"risky"*. I wrote a paper describing my [clonotypeR](https://www.bioconductor.org/packages/clonotypeR) package; it was rejected twice from Bioinformatics, but some reviewers comments ...
written 14 days ago by Charles Plessy1.5k
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Answer: A: Bioinformatics software distribution
... Here is my very biased point of view of member of the [Debian Med project](https://www.debian.org/devel/debian-med). > What is the best way from your experience to distribute bioinformatics software and what is the best way for you to get software? We distribute binary package, with names as c ...
written 14 days ago by Charles Plessy1.5k
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Comment: C: Error of bam-to-sam conversion using samtools
... Perhaps you can try running Samtool's regression tests to see if your installation works as expected ? Here is the [link to the test directory at version 1.2 on GitHub](https://github.com/samtools/samtools/tree/255f97daffd3a27d7b063e991a993f47ad6186cf/test). ...
written 16 days ago by Charles Plessy1.5k
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Comment: C: How to define a non differentially expressed gene?
... Let's imagine that T1 is a drug treatment in one kind of vehicle (solvent), T2 a drug treatment in a different vehicle, and C1 and C2 the use of each vehicle only (no drug dissolved). To rephrase your question are you saying that you have a design matrix like the following (triplicates not indicate ...
written 18 days ago by Charles Plessy1.5k

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