User: Charles Plessy

gravatar for Charles Plessy
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Posts by Charles Plessy

<prev • 37 results • page 1 of 4 • next >
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Answer: A: Behaviour of getCTSS on a CAGEset - extra reads?
... 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 4 months ago by Charles Plessy110
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Comment: C: Behaviour of getCTSS on a CAGEset - extra reads?
... Yes, please send me a minimal BAM file to my maintainer address. ...
written 4 months ago by Charles Plessy110
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How to make a GPos subclass that accept both UnstitchedGPos and StitchedGPos inputs?
... 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 ...
genomicranges written 4 months ago by Charles Plessy110 • updated 4 months ago by Hervé Pagès ♦♦ 14k
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Comment: C: Behaviour of getCTSS on a CAGEset - extra reads?
... 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 4 months ago by Charles Plessy110
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Comment: C: Does `clusterCTSS` and `aggregateTagClusters` sum raw-tag counts (and tpm) of th
... `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 6 months ago by Charles Plessy110
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Comment: C: Does `clusterCTSS` and `aggregateTagClusters` sum raw-tag counts (and tpm) of th
... `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 6 months ago by Charles Plessy110
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Comment: C: a problem from import CTSStable in CAGEr
... Hi, can you send me some sample data, by email or by opening an issue on GitHub ? ...
written 12 months ago by Charles Plessy110
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Comment: C: bam2CTSS function error from CAGEr package
... Perhaps you need to restart in a fresh R session so that the upgrade of MultiAsssayExperiment and SummarizedExperiment has its effect. ...
written 14 months ago by Charles Plessy110
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Comment: C: bam2CTSS function error from CAGEr package
... 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 14 months ago by Charles Plessy110
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Comment: C: bam2CTSS function error from CAGEr package
... As explained in point 3.1 of the vignette, you also need: library("MultiAssayExperiment") library("SummarizedExperiment") ...
written 14 months ago by Charles Plessy110

Latest awards to Charles Plessy

Scholar 2.5 years ago, created an answer that has been accepted. For A: CAGEr BAM files size issue
Supporter 3.8 years ago, voted at least 25 times.

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