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Code used to prepare disease data in survival format, calculate LRC score, data QC and preparation, and data analyses
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Longevity defined as the top 10% survivors ...
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Martin Larralde / Pyrodigal
GNU General Public License v3.0 onlyCython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
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Laros / fake-open
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Example interactive visualizations using Jupyter and Bokeh
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Martin Larralde / LightMotif
MIT LicenseA lightweight platform-accelerated library for biological motif scanning using position weight matrices.
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Martin Larralde / Peptides.py
GNU General Public License v3.0 onlyPhysicochemical properties and indices for amino-acid sequences (ported from R).
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Martin Larralde / Mini 3Di
GNU General Public License v3.0 onlyA NumPy port of the foldseek code for encoding protein structures to 3di.
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This pipeline takes paired-end fastq files, does a quick genome assembly on them (via Velvet + kmergenie), and predicts antibiotic resistance via abricate.
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Sam Nooij / R. gnavus MAGs from rCDI patients
BSD 3-Clause "New" or "Revised" LicenseGenerate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes
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