Trending repositories for topic computational-biology
DANCE: a deep learning library and benchmark platform for single-cell analysis
DANCE: a deep learning library and benchmark platform for single-cell analysis
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
A publicly-editable collection of open computational neuroscience resources
A Curated List of Computational Biology Datasets Suitable for Machine Learning
Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
DANCE: a deep learning library and benchmark platform for single-cell analysis
Interactive network visualization in Python and Dash, powered by Cytoscape.js
A list of schools and researchers in computational neuroscience
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Spatial alignment of single cell transcriptomic data.
A Curated List of Computational Biology Datasets Suitable for Machine Learning
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
A publicly-editable collection of open computational neuroscience resources
DANCE: a deep learning library and benchmark platform for single-cell analysis
Interactive network visualization in Python and Dash, powered by Cytoscape.js
A list of schools and researchers in computational neuroscience
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
A list of schools and researchers in computational neuroscience
A comprehensive library for computational molecular biology
A publicly-editable collection of open computational neuroscience resources
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
DANCE: a deep learning library and benchmark platform for single-cell analysis
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, p...
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
A Curated List of Computational Biology Datasets Suitable for Machine Learning
Fitness landscape exploration sandbox for biological sequence design.
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.
Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)
A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.
An interoperable Python framework for biomolecular simulation.
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, p...
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
A Curated List of Computational Biology Datasets Suitable for Machine Learning
Fitness landscape exploration sandbox for biological sequence design.
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Various utilities regarding Levenshtein transducers. (Java)
Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)
Mixed continous/categorical flow-matching model for de novo molecule generation.
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
A list of schools and researchers in computational neuroscience
A comprehensive library for computational molecular biology
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
A publicly-editable collection of open computational neuroscience resources
DANCE: a deep learning library and benchmark platform for single-cell analysis
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
Interactive network visualization in Python and Dash, powered by Cytoscape.js
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)
Mixed continous/categorical flow-matching model for de novo molecule generation.
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
An interoperable Python framework for biomolecular simulation.
A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.
A curated list of awesome computational cryo-EM methods.
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
Graph neural networks for molecular machine learning. Implemented and compatible with TensorFlow and Keras.
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Package for processing and analyzing glycans and their role in biology.
DANCE: a deep learning library and benchmark platform for single-cell analysis
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)