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medema-group / bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
GNU Affero General Public License v3.0
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Broken link for jupyter notebook scripts? #46

Open matinnuhamunada opened 2 years ago

matinnuhamunada commented 2 years ago

Hi @satriaphd, thanks for creating this amazing tool! I would like to learn and explore the SQL query data, and I thought maybe you already have some pointers in your Jupyter notebook scripts?

To access BiG-SLiCE's preprocessed data, (advanced) users need to be able to run SQL(ite) queries. Although the learning curve might be steeper compared to the conventional tabular-formatted output files, once familiarized, the SQL database can provide an easy-to-use yet very powerful data wrangling experience. Please refer to our publication manuscript to get an idea of what kind of things are able to be done with the output data. Additionally, you can also download and reuse some jupyter notebook scripts that we wrote to perform all analyses and generate figures for the manuscript.

Unfortunately, the link at https://bioinformatics.nl/~kauts001/ltr/bigslice/paper_data/scripts/ seems to be broken. Would you kindly fix the link and share the notebooks?

pjtorres commented 2 years ago

@matinnuhamunada I have some very simple SQL examples on how to explore your data here . Could help get you started.