eachanjohnson

eachanjohnson's Stars

• shap/shap

  A game theoretic approach to explain the output of any machine learning model.

  Language:Jupyter Notebook23k3.3k

• chaidiscovery/chai-lab

  Chai-1, SOTA model for biomolecular structure prediction

  Language:Python1.4k165

• jwohlwend/boltz

  Official repository for the Boltz-1 biomolecular interaction model

  Language:Python1.3k127

• recursionpharma/mole_public

  Recursion's molecular foundation model

  Language:Python301

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.3k603

• siddharthab/UMICollapse

  Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

  Language:Java2

• flairNLP/flair

  A very simple framework for state-of-the-art Natural Language Processing (NLP)

  Language:Python14k2.1k

• gradio-app/gradio

  Build and share delightful machine learning apps, all in Python. 🌟 Star to support our work!

  Language:Python34.3k2.6k

• cytoscape/ipycytoscape

  A Cytoscape Jupyter widget

  Language:Python27062

• SNU-CSSB/RF2-Lite

  Language:Python225

• ablab/IsoQuant

  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

  Language:Python15314

• mmp2/megaman

  megaman: Manifold Learning for Millions of Points

  Language:Python32368

• DLR-RM/stable-baselines3

  PyTorch version of Stable Baselines, reliable implementations of reinforcement learning algorithms.

  Language:Python9.2k1.7k

• kelwyres/Bactabolize

  Language:Python35

• jhkorhonen/MOODS

  MOODS: Motif Occurrence Detection Suite

  Language:C++9512

• npdeloss/meirlop

  Motif Enrichment In Ranked Lists Of Peaks

  Language:HTML71

• sanger-pathogens/Roary

  Rapid large-scale prokaryote pan genome analysis

  Language:Perl324189

• kblin/ncbi-acc-download

  Download files from NCBI Entrez by accession

  Language:Python1118

• ThomasCMcLean/LazyAF

  Code for LazyAF pipeline

  Language:Shell212

• pyg-team/pytorch_geometric

  Graph Neural Network Library for PyTorch

  Language:Python21.5k3.7k

• ncbi/datasets

  NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

  Language:Jupyter Notebook37142

• Opentrons/opentrons

  Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

  Language:Python429179

• RosettaCommons/RoseTTAFold

  This package contains deep learning models and related scripts for RoseTTAFold

  Language:Python2k440

• MatthijsHak/MetalDock

  Dock organometallic compounds to proteins/DNA/biomolecules

  Language:Python96

• aqlaboratory/openfold

  Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

  Language:Python2.8k551

• xqding/DCA

  Language:Python61

• baker-laboratory/RoseTTAFold-All-Atom

  Language:Python654118

• patrickbryant1/SpeedPPI

  Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning

  Language:Python7817

• mbhall88/NanoVarBench

  Evaluating Nanopore-based bacterial variant calling

  Language:Python15

• IBM/topography-searcher

  This Python package is designed for mapping the solution space of machine learning models. An understanding of the organisation of the solution space can answer important questions about the reproducibility, explainability and performance of ML methods.

  Language:Python125