User: Nicolas Delhomme

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320
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Sweden
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https://bioinformatics...
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Posts by Nicolas Delhomme

<prev • 73 results • page 1 of 8 • next >
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Comment: C: Adding information to the Installation document (https://www.bioconductor.org/in
... Hej Marcel! Thanks for the quick feedback. And yes, that solution works for me. I had actually not thought that BiocManager would have a vignette; I just pictured it like a wrapper around install.packages; my bad. Best, Nico --------------------------------------------------------------- Nicolas ...
written 9 days ago by Nicolas Delhomme320
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Adding information to the Installation document (https://www.bioconductor.org/install/)
... Hej! I was just upgrading from Bioc 3.7 to 3.8 and by reading the Installation instruction at https://www.bioconductor.org/install, I realised that it might be good if these were extended to: Detail how one can migrate from a previous version to the next; i.e. running BiocManager::install(version=" ...
website documentation written 9 days ago by Nicolas Delhomme320
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Answer: A: simpleRNASeq easyRNAseq warnings edgeR error
... Hej KGies! The warning about the non-common sequence levels can usually be safely ignored. It simply means that your BAM file and your annotation have sequences that are not in common, which most commonly happens 1) because 2 slightly different genome versions are used, 2) that an annotation/BAM fi ...
written 9 months ago by Nicolas Delhomme320
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Comment: C: Warning: missing reverse strand option in easyRNASeq.
... Dear Michael, Thank you for reporting on this. On one hand, luckily, my package is not main stream, so among the publications listed in PubMed, only one may be at risk. I will nonetheless contact the authors of all publication asap, as it is actually very hard to figure out the protocol that was us ...
written 16 months ago by Nicolas Delhomme320
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Comment: C: The input data for EBseq-HMM
... Hej Natalia! It sounds like you can use raw counts indeed. What confuses me here is the reference to RSEM, which is a tool to calculate expression estimate, but possibly it does also report raw counts. As a side note, I would advise you to look up how the raw count that you retrieved from the NCBI ...
written 2.1 years ago by Nicolas Delhomme320
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Comment: C: The input data for EBseq-HMM
... Hej Natalia! How did you obtain your raw counts? This is of importance here. The reason is that raw counts and expression estimates have different properties, and while technically you can probably give raw counts as input to EBseqHMM and would probably get an output, the results will very likely b ...
written 2.1 years ago by Nicolas Delhomme320
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Answer: A: The input data for EBseq-HMM
... Hej Natalia! For measuring expression: (i)  at the gene level, i.e. ignoring splice isoforms Raw counts represent "exact" counts, i.e. integer values. A raw count represents one mRNA fragment that was sequenced as one read. Counting these is very easy for unique regions, but becomes difficult whe ...
written 2.1 years ago by Nicolas Delhomme320
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Comment: C: SRAdb "outdated" sqlite db
... Hej Sean! Thanks! I'm managing the bioinformatics facility at the Umeå Plant Science Centre and we are planning to screen the SRA using SRAdb for datasets of interests that we could add to our Genome Browser resource plantgenie.org) on a regular basis. As such, we could contribute running the SQLit ...
written 2.2 years ago by Nicolas Delhomme320
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SRAdb "outdated" sqlite db
... Hej Jack Zhu and Sean Davis! I wanted to retrieve data that have recently been submitted (end of august) to the SRA, but I cannot do it using SRAdb, as the database I can fetch using getSRAdbFile() is "outdated", dating from early august: c("schema version", "creation timestamp")c("1.0", "2016-08-0 ...
sradb sqlite outdated written 2.2 years ago by Nicolas Delhomme320 • updated 2.2 years ago by Sean Davis21k
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Job: Bioinformatics First Research Engineer position
... The Department of Plant Physiology, which is part of Umeå Plant Science Centre, (www.upsc.se), has an open bioinformatics first research engineer position, full-time for one year, with possibility for extension. The working tasks principally are to provide bioinformatics support to the users of the ...

Latest awards to Nicolas Delhomme

Scholar 2.6 years ago, created an answer that has been accepted. For A: converting integer to numeric
Scholar 3.3 years ago, created an answer that has been accepted. For A: converting integer to numeric

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