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A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
"LightRAG: Simple and Fast Retrieval-Augmented Generation"
k-mer learning materials
MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
A complete alternative for Overleaf with VSCode + Web + Git Integration + Copilot + Grammar & Spell Checker + Live Collaboration Support. Based on GitHub Codespace and Dev container.
Jupyter notebooks that support my graph data science blog posts at https://bratanic-tomaz.medium.com/
A Whole Genome Alignment Visualization Tool for the Web
A data index and query language over Markdown files, for https://obsidian.md/.
Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
Host repository for The Turing Way: a how to guide for reproducible data science
Jupyter server extension to sync a git repository one-way to a local path
A GitHub action to build data science environment images with repo2docker and push them to registries.
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Phage Annotation using Protein Structures
General purpose Snakemake pipeline for PanTools v4.
Bilingual Language Model for Protein Sequence and Structure
An updated pipeline for pangenome investigation
BlackHole is a modern macOS audio loopback driver that allows applications to pass audio to other applications with zero additional latency.
Topology weighting by iterative sampling of sub-trees
Customize your Zotero workflow.
Automatic Generation of Visualizations and Infographics using Large Language Models
Unsupervised text tokenizer for Neural Network-based text generation.