User: kevin.rue

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kevin.rue230
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University of Oxford
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1 week ago
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5 years, 1 month 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 • 48 results • page 1 of 5 • next >
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Answer: A: Obtain the first gene expression heatmaps from GOexpress package gene ontology e
... Hi Antonio, Thanks for your question and the minimum reproducible example using the documentation. To plot heatmaps automatically, you can use a `for` loop that iterates over a vector of GO identifiers. For instance, in the block below, I identify the top 5 most significant GO categories (i.e., so ...
written 8 days ago by kevin.rue230
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Answer: A: 'GO_analyse' function error
... In your post, your key command is: ``` results <- GOanalyse(eSet = z, f = "condition",biomartdataset= "hsapiensgene_ensembl") ``` There are two errors in this command: - `biomartdataset ` should be `biomart_dataset` - `hsapiensgene_ensembl ` should be `hsapiens_gene_ensembl ` Recommendations ...
written 6 weeks ago by kevin.rue230
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Comment: C: 'GO_analyse' function error
... Hi, Your code is very difficult to read without appropriate formatting. Please use the online editor to help you format text and code clearly, which helps me help you. See below for a rapid cleanup and comments. Note that you can use [`reprex::reprex({...})`][1] to produce code and output that you ...
written 6 weeks ago by kevin.rue230
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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 4 months ago by kevin.rue230 • updated 4 months ago by Aaron Lun25k
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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 16 months ago by kevin.rue230
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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 21 months ago by kevin.rue230
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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 21 months ago by kevin.rue230
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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 21 months ago by kevin.rue230
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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 2.3 years ago by kevin.rue230
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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 2.3 years ago by kevin.rue230

Latest awards to kevin.rue

Popular Question 15 months ago, created a question with more than 1,000 views. For Error building R Markdown v2 document
Scholar 2.6 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 2.6 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Teacher 2.6 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 2.7 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 3.6 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 3.6 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Autobiographer 3.7 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 4.0 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 4.0 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step
Scholar 4.0 years ago, created an answer that has been accepted. For A: GOexpress error at pValue_GO step

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