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An opinionated list of awesome Python frameworks, libraries, software and resources.
Open source code for AlphaFold.
A Python implementation of global optimization with gaussian processes.
🌎 Simple and ready-to-use tutorials for TensorFlow
Visual analysis and diagnostic tools to facilitate machine learning model selection.
💫 Beautiful spinners for terminal, IPython and Jupyter
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Collection of bioinformatics training materials
RNAseq analysis notes from Ming Tang
ML-Ensemble – high performance ensemble learning
Terminal string styling done right, in Python 🐍 🎉
Customizable workflows based on snakemake and python for the analysis of NGS data
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Virus Identification By iteRative ANnoTation
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Library to build command line interfaces based on Click. It extends click with: option groups, constraints (e.g. mutually exclusive params), command aliases, help themes, "did you mean ...?" sugges…
Multi-task and masked language model-based protein sequence embedding models.
Python package to study microbial communities using metabolic modeling.
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Sparse Cooccurence Network Investigation for Compositional data