User: kevin.rue

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kevin.rue220
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220
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Location:
University of Oxford
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Last seen:
1 week, 3 days ago
Joined:
4 years, 9 months ago
Email:
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 • 45 results • page 1 of 5 • next >
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scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
... Hi, Please see the `reprex` below. This involves a few packages (scater, DelayedArray, BiocSingular), and I'm not exactly sure in which one the issue is taking place. Any help is appreciated! ```r suppressPackageStartupMessages(library(TENxPBMCData)) tenx_pbmc3k <- TENxPBMCData(dataset="pbmc3k" ...
scater delayedarray biocsingular written 5 weeks ago by kevin.rue220 • updated 4 weeks ago by Aaron Lun24k
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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 12 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 17 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 17 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 17 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 23 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 23 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 2.3 years 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 2.3 years 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 2.4 years ago by kevin.rue220

Latest awards to kevin.rue

Scholar 2.3 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 2.3 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Teacher 2.3 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
Teacher 2.4 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 3.3 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 3.3 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 3.7 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 3.7 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 3.7 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step

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