User: t.kuilman

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t.kuilman710
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710
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Netherlands
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1 week, 2 days ago
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3 years, 7 months ago
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t********@nki.nl

Posts by t.kuilman

<prev • 41 results • page 1 of 5 • next >
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Answer: A: RNA-seq data from human tumors in mice (PDTX)
... As a matter of fact, a colleague of mine (Oscar Krijgsman) just wrote a new tool specifically for this type of analysis. It is based on the principle of aligning the reads to both human and mouse reference genomes, and then assigning reads to human / mouse based on their alignment qualities to these ...
written 8 weeks ago by t.kuilman710
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Comment: C: Entrez Direct to retrieve Protein and Coding sequences from NCBI accesion
... An R-based solution would be to use the `Bioconductor` package `BiomaRt`; please see my post [here][1]. Since you have the exact chromosomal position already, you can easily covert this to sequences. You can find the appropriate filters (chromosome, start and end position) using `listFilters(ensembl ...
written 9 weeks ago by t.kuilman710
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Answer: A: What's more clear, loops or functions?
... My personal view is that using `apply` type of functions is actually the cleaner way and is also easier to read. For instance, there is no need for declaring any extra 'dummy' variables that get filled during the looping. A simple way of reading tables and assembling those into a single `data.frame` ...
written 9 weeks ago by t.kuilman710
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Answer: A: how to deal with sra files which can generate three fastq files?
... Please see my previous [post][1]: this is due to the fact that BOTH paired and unpaired reads are included in these sra files. Using the `--split-files` option does not work since this would lead to fastq-files that are incomplete. What you did is correct; simply use the files ending with `_1` and ` ...
written 9 weeks ago by t.kuilman710
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Comment: C: Download STRING database with Protein name
... As pointed out [here][1] and [here][2], this is likely due to a server being temporarily down. I am not sure where you are, but you can try any of these mirrors https://www.ensembl.org/ https://uswest.ensembl.org/ https://useast.ensembl.org/ https://asia.ensembl.org/ by adding the arguments `ho ...
written 9 weeks ago by t.kuilman710
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Answer: A: Download STRING database with Protein name
... Here is an R-based solution: > test [1] "ENSP00000263431" "ENSP00000353863" "ENSP00000342026" "ENSP00000240874" > library("biomaRt") > ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > conversion.table <- getBM(attributes = c("ensembl_peptide_i ...
written 9 weeks ago by t.kuilman710
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Answer: A: How to calculate rooted bifurcating tree shapes
... An R implementation would be as follows: S <- NULL for (n in 1:19) { if (n == 1) { S <- 1 } else if (n%%2 == 0) { S <- c(S, sum(S[seq_len((n/2)-1)] * S[(n-1):(n-((n/2)-1))]) + S[n/2] * (S[(n/2)]+1)/2) } else { ...
written 10 weeks ago by t.kuilman710
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Answer: A: R "object not found"
... First, it would be helpful if you provide the complete output from your console, since it will help figuring out the details of the problem. The error you mention can only arise from `dim()`: > dim(non.existing.variable) Error: object 'non.existing.variable' not found This only occurs ...
written 10 weeks ago by t.kuilman710
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Comment: C: Merging a list of genes/features within genomic ranges
... You seem to be on the right way, and using `GRanges` would be the principled way to do this in R. It would be helpful to provide what you have tried already, and ideally a sample of the `GRanges` objects that you would like to merge (you can do that using `dput()`) ...
written 10 weeks ago by t.kuilman710
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Answer: A: Method to get all possible combinations of genotypes for a group of SNPs
... Here is a R-based solution using `expand.grid()`: > SNP1 [1] "A" "T" > SNP2 [1] "C" "G" > SNP3 [1] "T" "A" > expand.grid(SNP1_alleleA = SNP1, SNP1_alleleB = SNP1, SNP2_alleleA = SNP2, SNP2_alleleB = SNP2, SNP3_alleleA = SNP3, SNP3_alleleB = ...
written 10 weeks ago by t.kuilman710

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