khmer

github.com/dib-lab/khmer

k-mer counting, filtering, and graph traversal.

Sourced from

  • Awesome Scientific Pythongithub.com/dib-lab/khmer

Related resources

Comprehensive collection of 125+ ready-to-use scientific skill modules for Claude AI across bioinformatics, cheminformatics, clinical research, ML, and materials science

Active27.8K1 day ago
Python
MIT

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science with 140+ ready-to-use skills and 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Antigravity, and the open Agent Skills standard (K-Dense-AI, 26K+ stars, 2025)

Active26.5K1 week ago
Python
MIT

Deep learning-based variant caller

Active3.7K2 months ago
Python
BSD-3-Clause

Therapeutics Data Commons: 66 AI-ready datasets across 22 drug discovery tasks with 29 leaderboards, covering target identification, molecular generation, ADMET prediction, and clinical trial outcomes (Harvard MIMS, NeurIPS 2021/2024)

Idle1.3K11 months ago
Jupyter Notebook
MIT

Fast and accurate protein structure search using a learned 3Di structural alphabet (VQ-VAE) that discretizes tertiary interactions into structural tokens, enabling protein-universe-scale structural alignment at sequence-search speeds (4-5 orders of magnitude faster than DALI/TM-align) and underpinning many AI4S tools such as SaProt, ESMAtlas search, and AFDB clustering pipelines (Steinegger Lab, Nature Biotechnology 2023)

Active1.2K4 weeks ago
C
GPL-3.0

Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.

Active1.2K2 weeks ago
Jupyter Notebook
MIT