User: Alexandre Drouin

Reputation:
50
Status:
Trusted
Location:
Montreal, Canada
Website:
http://graal.ift.ulava...
Twitter:
alexandredrouin
Scholar ID:
Google Scholar Page
Last seen:
3 months, 2 weeks ago
Joined:
2 years, 8 months ago
Email:
a******@gmail.com

PhD Candidate @ Université Laval

Machine learning + Computational biology

Posts by Alexandre Drouin

<prev • 9 results • page 1 of 1 • next >
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Answer: A: error while creating kover dataset from fastq
... Sorry for the late reply. It's the first time that I see this exception come out of DSK (the k-mer counter used by kover). Could you please show me a few lines of genomes.tsv and metadata.tsv? If you're able to share one of your fastq.gz files it would also be very useful. Thanks! Alex ...
written 4 months ago by Alexandre Drouin50
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Answer: A: Additional data for different isolates and antibiotics
... Hi! Yes, you can definitely get more data to train kover. The best source for antibiotic resistance datasets is the PATRIC database: https://www.patricbrc.org. I created a Python package to extract data from it: https://github.com/aldro61/patric_tools. Particularly, have a look at this script that ...
written 10 months ago by Alexandre Drouin50
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Comment: C: Kover - order of metadata
... It would definitely help me look into this if you were able to share your data. Would you be able to upload it to a server (e.g.: https://mega.nz/) and share the link? Also, can you include the kover commands that you are using to create and split the data? Did you set the random seed parameter in ...
written 2.1 years ago by Alexandre Drouin50
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Comment: C: kover installation problem: include could not find load file: GatbCore
... You're right. Sorry about that! ...
written 2.1 years ago by Alexandre Drouin50
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Comment: C: kover installation problem: include could not find load file: GatbCore
... Could you please add the "kover" tag to your post? ...
written 2.1 years ago by Alexandre Drouin50
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Answer: A: kover installation problem: include could not find load file: GatbCore
... Hi Huan, Try using: > git clone --recursive https://github.com/aldro61/kover.git GATB is included as a submodule in Kover and when you don't use the "recursive" option, it doesn't get cloned. This is why the installer cannot find the GatbCore files. Let me know if it works! Alex ...
written 2.1 years ago by Alexandre Drouin50
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Comment: C: Kover will provide support via Biostars
... Hi, like WouterDeCoster suggested, please create a new post with "kover" as a tag and post the full error messages. Also, please ensure that you have installed all the software dependencies: https://aldro61.github.io/kover/doc_installation.html#prerequisites. You do not need root privilege to run Ko ...
written 2.1 years ago by Alexandre Drouin50
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Comment: C: Kover will provide support via Biostars
... Thanks for the suggestion! I added an example in the description and a link to a hands-on tutorial. ...
written 2.7 years ago by Alexandre Drouin50
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News: Kover will provide support via Biostars
... Kover is an [out-of-core](https://en.wikipedia.org/wiki/Out-of-core_algorithm) implementation of the [Set Covering Machine](http://www.jmlr.org/papers/volume3/marchand02a/marchand02a.pdf) algorithm that has been tailored for genomic biomarker discovery. Given two groups of phenotipically distinct ...
news kmer machine learning kover written 2.7 years ago by Alexandre Drouin50 • updated 2.1 years ago by hfan2210

Latest awards to Alexandre Drouin

Popular Question 10 months ago, created a question with more than 1,000 views. For Kover will provide support via Biostars
Scholar 2.1 years ago, created an answer that has been accepted. For A: kover installation problem: include could not find load file: GatbCore
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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