User: mathias.heydt

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Posts by mathias.heydt

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Is there public (DNA methylation) data on circulating cell-free DNA - why not?
... In the near future, I will have to deal with circulating cell-free DNA in the context of finding cancer biomarkers - I have read up on methylation, biomarkers, cancer, though I must admit I haven't read too much about cfDNA yet. In this context, it seems strange that I can't find (450k) methylation ...
epigenetics circulating cell-free dna biomarker written 28 days ago by mathias.heydt60 • updated 28 days ago by Kevin Blighe19k
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Comment: C: TCGA calling pipeline query
... Have you tried looking [here][1]? I found it difficult to find my way to all of these pages, but maybe your answer is in there. [1]: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#somatic-variant-calling-workflow ...
written 6 weeks ago by mathias.heydt60
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Answer: A: Differential methylation analysis
... If you have already downloaded your data, you can also make use of the ChAMP package. https://bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html It makes use of the limma package, so you'd use linear models instead of regular t-tests to find DMPs. [This section][1] show you ...
written 6 weeks ago by mathias.heydt60
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Comment: C: Data Discrepency from TCGA-GDC portal and GDC firehose
... You are using TCGAbiolinks already, aren't you then also retrieving the full ids for the clinical data? This should help you: I assume you're starting with: query <- GDCquery("yourquery") Then just type: getResults(query, cols = c("cases", "tissue.definition")) ...
written 7 weeks ago by mathias.heydt60
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Comment: C: TCGABioLinks how to set Sample conditions?
... You're doing something totally different from the example, and different from your first question anyway. The MAE is a separate class, and in the example, they create it using summarizedExperiment class objects (lusc.exp and lusc.met) I'm not using these classes, so I can't look into it for you, but ...
written 9 weeks ago by mathias.heydt60
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Comment: C: TCGABioLinks how to set Sample conditions?
... Yeah, like I said in my answer, if you know the barcodes of your samples in set A and set B, you can just specify them; In the example they specify their sets with the TCGAquery_samples function. You don't need to do that. Just list the barcodes directly. dataSmTP is just a variable name, so you can ...
written 9 weeks ago by mathias.heydt60
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Comment: C: help with GDCprepare
... I was able to download and prepare it. Could be the biomart servers were down, so try again?. And if it still isn't working, you could consider downloading the developer version of tcgabiolinks if you haven't done that. Alternatively, it could be due to the fact that you're asking legacy data. Do yo ...
written 9 weeks ago by mathias.heydt60
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Answer: A: TCGABioLinks how to set Sample conditions?
... Does your example work? I recently started working with TCGAbiolinks aswell, and some functions throw errors, I haven't got the time to test it out for you though. In any case: dataSmTP <- TCGAquery_SampleTypes(barcode = samplesDown, typesample = "TP") ...
written 9 weeks ago by mathias.heydt60
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Comment: C: Transfer of MHC-I, MHC-II epitope prediction to non-model organism (fish)
... Yeah if you want *reliable* predictions, you'd need binding affinities of the salmon alleles. But I was told there exist other prediction tools that predict binding affinities based on the protein sequence of your allele. So you could download the protein FASTA on ipd-mhc db and feed it to these to ...
written 12 weeks ago by mathias.heydt60
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Comment: C: Transfer of MHC-I, MHC-II epitope prediction to non-model organism (fish)
... Hi Michael There exist some tools that try to predict binding affinity if you feed protein sequences aswell, but unless the binding affinity for fish (your salmon⁾ have been taken up in an existing predicting tool you're out of luck. You could start making your own tool if there are even binding af ...
written 12 weeks ago by mathias.heydt60

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