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 • 71 results • page 1 of 8 • next >
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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 7 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 14 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 23 months 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 23 months 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 23 months 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 24 months 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 24 months ago by Nicolas Delhomme320 • updated 24 months 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 ...
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Job: Bioinformatics Research Engineer position
... The Department of Plant Physiology, which is part of Umeå Plant Science Centre, (www.upsc.se), has an open bioinformatics 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 UPSC b ...
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Answer: A: converting integer to numeric
... Hej Fereshteh Izadi! At the moment, your mycounts object is a data.frame mixing both characters (the first column) and integer/numeric values (your second to fourth columns). Depending on what you want to do with your object, e.g. coerce it as a matrix using as.matrix(mycounts) you will get the er ...
written 2.7 years ago by Nicolas Delhomme320

Latest awards to Nicolas Delhomme

Scholar 2.4 years ago, created an answer that has been accepted. For A: converting integer to numeric
Scholar 3.1 years ago, created an answer that has been accepted. For A: converting integer to numeric

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