## User: Charles Plessy

Reputation:
110
Status:
Trusted
Location:
Japan
Last seen:
1 month, 3 weeks ago
Joined:
4 years, 4 months ago
Email:
c***********@plessy.org

#### Posts by Charles Plessy

<prev • 37 results • page 1 of 4 • next >
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... Hi Sara, you are right, it seems that the correctSystematicG option is badly broken. I do not have time to fix this in the short term, so if your results do not critically depend on it, may I suggest to turn it to FALSE ? ...
written 3 months ago by Charles Plessy110
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... Yes, please send me a minimal BAM file to my maintainer address. ...
written 3 months ago by Charles Plessy110
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... Hello, in the CAGEr package, I defined a CTSS (_CAGE Transcription Start Site_) subclass of GPos as follows:  .CTSS <- setClass("CTSS", contains = "GPos")  My goal is to add some type safety to my functions, to prevent myself to run them on GPos objects that are not transcription sta ...
written 3 months ago by Charles Plessy110 • updated 11 weeks ago by Hervé Pagès ♦♦ 14k
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... Hello, the getCTSS function applies several filters on the data, and when using BAM files as input it will also attempt to correct the *"G bias"* of CAGE, as explained in the function's documentation. If this does not answer your question, can you give me a reproductible test case illustrating y ...
written 3 months ago by Charles Plessy110
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... CTSStagCountGR works at the level of individual samples, so it needs a sample argument. If you want all CTSS positions, you can use CTSScoordinatesGR If you want an expression table, you can use CTSStagCountDF. ...
written 4 months ago by Charles Plessy110
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... clusterCTSS and aggregateTagClusters calculate both the raw tag count and the normalised expression scores of the consensus clusters. It is not possible to skip the calculation of the normalised expression scores (at this point, I am not sure if this would bring a significant performance advanta ...
written 4 months ago by Charles Plessy110
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... Hi, can you send me some sample data, by email or by opening an issue on GitHub ? ...
written 10 months ago by Charles Plessy110
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... Perhaps you need to restart in a fresh R session so that the upgrade of MultiAsssayExperiment and SummarizedExperiment has its effect. ...
written 12 months ago by Charles Plessy110
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... Judging from their version numbers, the SummarizedExperiment and MultiAssayExperiment packages seem quite outdated on your system. Can you update them to the current Bioconductor release ? ...
written 12 months ago by Charles Plessy110
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... As explained in point 3.1 of the vignette, you also need: library("MultiAssayExperiment") library("SummarizedExperiment") ...
written 12 months ago by Charles Plessy110

#### Latest awards to Charles Plessy

Scholar 2.3 years ago, created an answer that has been accepted. For A: CAGEr BAM files size issue
Supporter 3.6 years ago, voted at least 25 times.

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