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PhinchApp / Phinch

Phinch is a data visualization framework aimed at promoting novel explorations of large biological datasets (microbiomes, metagenomes, etc.). Features include support for HDF5 and JSON BIOM files, retooled visualizations, improved image export and sharing, and the ability to work offline.
BSD 2-Clause "Simplified" License
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Biom format from kraken-biom is not working #15

Closed LeonardosMageiros closed 1 year ago

LeonardosMageiros commented 4 years ago

Hi,

I have analysed some metagenomic samples using Kraken2 and I would like to visualise my taxonomic profiles using Phinch. I used the kraken-biom tool (https://github.com/smdabdoub/kraken-biom) to transform the kraken output to biom format but when I upload the files to Phinch the biom files are not validated.

Have you ever faced this issue before? I would appreceate any suggestions

Thank you in advance.

Best Leonardos

heather340 commented 3 years ago

I am having the same issue. Have you been able to resolve anything?

Thanks!

smdabdoub commented 2 years ago

@LeonardosMageiros @heather340 Hi all, I am the author of kraken-biom. I've recently integrated some code to add metadata to the biom tables created by kraken-biom. This was reported as an issue, and the update should fix the problem you're having.

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