User: kevin.rue

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kevin.rue220
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University of Oxford
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2 months, 3 weeks ago
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4 years ago
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k*********@gmail.com

Computational Biologist.

  • 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 • 44 results • page 1 of 5 • next >
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plotTracks issue with BAM files (ChIP-seq, paired)
... Hello! I am trying to plotTracks reads mapped to a ChIP-seq peak region for a set of 6 BAM files (3 ChIP, 3 inputs) that contain paired-end reads. If I subset to certain samples, it works as per this screenshot: https://www.dropbox.com/s/s71s9wu8v8vpshb/Screenshot%202018-06-19%2014.09.19.png?dl=1 ...
gviz written 3 months ago by kevin.rue220
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Comment: C: GOexpress - Trouble with subset_scores result (<0 rows>)
... Thank you for your feedback. I'm glad I could solve your issue and I'll see what I can do to address it in the future. The resource that you linked will be useful for this. Can I ask you to click the button that  "accepts" my answer above, so that future visitor to the post can identify the solution ...
written 7 months ago by kevin.rue220
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Answer: A: GOexpress - Trouble with subset_scores result (<0 rows>)
... Dear Sina. Having looked at the objects that you sent me, I can say that this is due to some hard-coded assumptions in the code of GOexpress. It expects values in the column namespace_1003 to be one of c("biological_process","molecular_function","cellular_component"). To clarify, BP, MF, and CC are ...
written 7 months ago by kevin.rue220
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Comment: C: GOexpress - Trouble with subset_scores result (<0 rows>)
... Dear Sina, Any chance you can email me a minimal reproducible example (MWE) of the issue, so that I can examine the issue myself? If possible the input list that you are working with?  You can export the list as follows: ``` saveRDS(name_of_your_list, "file_name.rds") ``` and email me the file. My ...
written 7 months ago by kevin.rue220
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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 14 months ago by kevin.rue220
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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 14 months ago by kevin.rue220
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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 18 months ago by kevin.rue220
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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 18 months ago by kevin.rue220
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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 20 months ago by kevin.rue220
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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 2.1 years ago by kevin.rue220

Latest awards to kevin.rue

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
Teacher 18 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 20 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 2.5 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 2.5 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 2.9 years 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 2.9 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 2.9 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step

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