User: kevin.rue

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kevin.rue200
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University of Oxford
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4 weeks, 1 day ago
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k*********@gmail.com

Bioinformatician.

  • Research associate: Bioinformatics/Biostatistics of idiopathic pulmonary artery hypertension (IPAH) at Imperial College London (United-Kingdom) [2015-2018]
  • PhD: Wellcome Trust Computational Infection Biology PhD Programme at University College Dublin (Ireland) [2011-2015]
  • Master's Degree / Ingénieur diplômé: Bioengineering, major Bioinformatics and Modelling for Biology at Polytech'Nice in Sophia-Antipolis (France) [2008-2011]

 

Research and contributions to projects using the following platforms:

  • Transcriptomics (Affymetrix® GeneChip® Bovine Genome array, Illumina® RNA-sequencing)
  • Genomics (Illumina® Whole Genome Sequencing)
  • Metabolomics (Metabolon®, Mass spectrometry)
  • Proteomics (Somalogic®)

 

Posts by kevin.rue

<prev • 40 results • page 1 of 4 • next >
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Answer: A: Monocle causes R session to crash
... Hi all, It's really weird, but monocle is crashing on me too, during a subsetting operation, or rather the assignment of the subsetting to a new variable. I have an object called `bds` that I obtained from `buildBranchCellDataSet`. Basically: bds <- buildBranchCellDataSet(HSMM, branch_point = ...
written 9 weeks ago by kevin.rue200
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Documentation of "branch_states" and "branch_labels" arguments
... Dear developers, First of all thank you for the great work behind `monocle`. Much appreciated! I am using `BEAM`, `plot_genes_branched_heatmap`, and `plot_genes_branched_pseudotime` at the moment. I am struggling to interpret which two branches are compared, and how to control it. First question: ...
monocle written 9 weeks ago by kevin.rue200
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Comment: C: heatmap of genes based on enriched GO categories
... Thanks! I am always more than happy to take suggestions to further develop GOexpress; in fact, I believe it got to the stage where more than half the features are based on feedback, and I like it this way :) I must admit: there are many ways in which I would like to consolidate GOexpress before ext ...
written 6 months ago by kevin.rue200
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Answer: A: heatmap of genes based on enriched GO categories
... Dear Bodgan, I don't have much to add after Gordon :) I'll just point out that GOexpress was intended to visualise the expression of genes associated with a single GO category. As Gordon just stated, advanced customisation is generally done by hand. Regarding customised heat map, you might want t ...
written 6 months ago by kevin.rue200
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Answer: A: Contrasts in GOexpress analysis?
... Dear Martin, "I'm having difficulty understanding what the returned pvalues because there's no mention what what the contrasts are. [...] It appears that the pvalue returned is for the overall effect a GO term across all factors (e.g., sort of like an F statistic)." Indeed you are right: GOexpress ...
written 8 months ago by kevin.rue200
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Comment: C: info(header(vcf)) remembers fields not imported: bugfix?
... Thank you. I suspected so, and it makes sense. In my use case however, I prefer to keep header and data synchronised, for a few reasons: My package does not need to know the possible fields in the original file As a consequence, I keep a cleaner object without unnecessary grime (no offense! just ...
written 13 months ago by kevin.rue200
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info(header(vcf)) remembers fields not imported: bugfix?
... Dear maintainer, I notice a slightly strange behaviour of readVcf when ScanVcfParam(info=). It seems that the imported VCF object somehow retains memories of the original VCF header (in the file), while the data was effectively dropped. After import, the show method seems fine (header and INFO st ...
variantannotation written 13 months ago by kevin.rue200
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parnotes rev. 2 breaks Bioconductor LATEX Style 2.0
... Dear Maintainer, In restrospect, I probably should have posted here before opening an issue on GitHub  I believe a recent release of parnotes (rev. 2, https://www.ctan.org/pkg/parnotes) has broken the Bioconductor LATEX Style 2.0. While a day ago Travis CI was perfectly happy compiling my package ...
biocstyle written 13 months ago by kevin.rue200 • updated 13 months ago by Andrzej Oleś670
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Comment: C: Error building R Markdown v2 document
... Sorry for using the User mailing list.  Installing pandoc and pandoc-citeproc solved the issue perfectly. Thanks! My DESCRIPTION file was set up as recommended in the linked document. I just hadn't found the information about the requirement for pandoc and co. :) Thanks again for the quick answer ...
written 14 months ago by kevin.rue200
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Error building R Markdown v2 document
... Hi, This is certainly an issue that can be addressed when I submit my package to the tracker (soon-ish), but maybe it can also benefit other developers if I post it here first. I have started writing an extremely basic R Markdown vignette (title page and sessionInfo) in R Studio, starting from the ...
biocstyle written 14 months ago by kevin.rue200 • updated 14 months ago by Martin Morgan ♦♦ 20k

Latest awards to kevin.rue

Scholar 6 months ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is it common to get all 0 values when running the randomForest step in GOexpress
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is it common to get all 0 values when running the randomForest step in GOexpress
Scholar 18 months ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 18 months ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Is it common to get all 0 values when running the randomForest step in GOexpress
Scholar 23 months ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 23 months ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step

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