User: andrea.rau

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andrea.rau50
Reputation:
50
Status:
New User
Location:
INRA / Jouy en Josas, France
Website:
http://www.andrea-rau....
Twitter:
andreamrau
Last seen:
1 day, 19 hours ago
Joined:
3 years ago
Email:
a*********@inra.fr

Statistician + author of some R (ebdbNet, HTSCluster, HTSDiff) & Bioconductor (HTSFilter, coseq) packages

Posts by andrea.rau

<prev • 6 results • page 1 of 1 • next >
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Answer: A: function meaning(on.index <- which(filter$on == 1))
... In this code, the HTSFilter package is being used to filter the data (contained in the cds object) to remove genes with relatively low counts across samples using a data-driven filtering threshold. The HTSFilter function returns both the filtered data themselves (contained in filter$filteredData, wh ...
written 4 months ago by andrea.rau50
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Comment: C: Running HTSFilter in paralell
... After a longer delay than expected (my apologies!), HTSFilter now implements (as of Bioconductor 3.4, version 1.14.0) the option for parallel calculations through the BiocParallel package. There are now two additional optional arguments in calls to HTSFilter: parallel (TRUE/FALSE) and BPPARAM to spe ...
written 12 months ago by andrea.rau50
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Answer: A: Error when trying to run HTSFilter
... If you have one condition that has a single replicate, I would think there are two options you could try: 1) For the purposes of filtering via HTSFilter, you could just assimilate that singleton sample with the replicates from the closest/most similar condition (i.e., just in the filtering step, no ...
written 12 months ago by andrea.rau50
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Comment: C: Error when trying to run HTSFilter
... Hi and thanks for your question. I think I'll need some additional information, as I'm not currently able to replicate your error. In particular, could you send me a minimal reproducible example that throws the same error that you're seeing so that I can work off that? Also, what version of HTSFilte ...
written 13 months ago by andrea.rau50
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Answer: A: Running HTSFilter in paralell
... Ok, I will work on adding the possibility of parallel calculations to HTSFilter. It may take me a couple of weeks to get around to it, but I will let you know when it is ready for testing in the development version. Thanks again for the feedback! Best, Andrea ...
written 22 months ago by andrea.rau50
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Answer: A: Running HTSFilter in paralell
... Hi Richard, If HTSFilter is taking a while to run, I'm guessing that it's because you have a fairly large number of samples -- right? The method in HTSFilter is extremely parallelizable since for a given filtering threshold, the Jaccard similarity index is calculated in a loop for all possible pair ...
written 22 months ago by andrea.rau50

Latest awards to andrea.rau

Scholar 22 months ago, created an answer that has been accepted. For A: Error when trying to run HTSFilter
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.

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