User: WouterDeCoster

gravatar for WouterDeCoster
Reputation:
110
Status:
Trusted
Location:
Antwerp, Belgium
Twitter:
wouter_decoster
Last seen:
3 months ago
Joined:
2 years, 1 month ago
Email:
d*************@gmail.com

I'm a PhD student with strong interest in bio-informatics, but followed master in biochemistry prior to starting my PhD. I mainly work on data from genome sequencing, whole exome sequencing, targeted resequencing, RNA-seq and Nanopore Sequencing using MinION and (soon!) PromethION. I have most experience with Python but starting to get rather efficient in R.

Posts by WouterDeCoster

<prev • 28 results • page 1 of 3 • next >
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Expression deconvolution using PSEA: applicable to RNA-seq?
... I came across the PSEA package which is used for computational deconvolution of microarray expression datasets. Their paper demonstrates its usage on human brain microarray data. The paper and reference manual mention microarray, but I wonder if the same method is applicable to RNA-seq data? Consid ...
rnaseq deconvolution psea written 5 months ago by WouterDeCoster110
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Comment: C: extracting the exons coordinates on hg38
... Cross posted: https://www.biostars.org/p/276608/ ...
written 9 months ago by WouterDeCoster110
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Comment: C: How to normalize Microarray expression data?
... Have you tried asking Dr. Google? Googling `microarray data analysis using r` brings up this Bioconductor guide as first hit. ...
written 9 months ago by WouterDeCoster110
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Comment: C: R: error while reading .h5 files from R using rdhf5 package
... Is the file in your current directory? ...
written 13 months ago by WouterDeCoster110
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Comment: C: installing package from bioconductor
... My first guess would be that the space in the path is the problem. ...
written 13 months ago by WouterDeCoster110
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Comment: C: Problem with readFast5Summary in IONiseR related to HDF5
... I notice you have a space in the path to your data, which is generally not a good idea. It might be unrelated to this issue (but I would suggest you to test it anyway). ...
written 15 months ago by WouterDeCoster110
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Comment: C: Error in Heatmap...
... My first guess would be to try without spaces in the filename. That's usually something you want to avoid. ...
written 16 months ago by WouterDeCoster110
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Comment: C: Error in valcano plot
... It's probably helpful to show the code you used for the volcano plot and for adding labels to the volcano, too. ...
written 16 months ago by WouterDeCoster110
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Comment: C: IONiseR error when trying to call readFast5Summary on fast5 reads
... Is your data recent? There has been an update of the format. ...
written 16 months ago by WouterDeCoster110
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Answer: A: featureCounts creating fragments and high NoFeatures value
... Based on my understanding: STAR is reporting percentages on the number of reads received as input of STAR (so in the fastq files). In contrast, featureCounts is reporting percentages on the number of alignments, which is, due to multimapping, higher than the number of reads. For STAR one fastq is ...
written 17 months ago by WouterDeCoster110

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Supporter 12 months ago, voted at least 25 times.
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