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249 search results found

Cs Video Courses ⭐ 62,887

List of Computer Science courses with video lectures.

Awesome Deepbio ⭐ 1,467

A curated list of awesome deep learning applications in the field of computational biology

Graphein ⭐ 932

Protein Graph Library

Scikit Bio ⭐ 833

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

3dmol.js ⭐ 720

WebGL accelerated JavaScript molecular graphics library

Opensim Core ⭐ 712

SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

Diffdock ⭐ 686

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

Biopandas ⭐ 673

Working with molecular structures in pandas DataFrames

A high-performance, Pythonic language for bioinformatics

A Go package for engineering organisms.

Dash Cytoscape ⭐ 555

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Open Computational Neuroscience Resources ⭐ 481

A publicly-editable collection of open computational neuroscience resources

Openchem ⭐ 450

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

Cobrapy ⭐ 414

COBRApy is a package for constraint-based modeling of metabolic networks.

A toolbox for integrated information theory.

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

Jupyter_dock ⭐ 215

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Geodiff ⭐ 211

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

Deep Rules ⭐ 198

Ten Quick Tips for Deep Learning in Biology

UCSC Genome Browser source tree. Stable branch: "beta".

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Biosyntax ⭐ 184

Syntax highlighting for computational biology

Gerardus ⭐ 180

Computational biology and medical image processing scripts and programs

Deep_learning_papers ⭐ 175

A place to collect papers that are related to deep learning and computational biology

Awesome Computational Neuroscience ⭐ 166

A list of schools and researchers in computational neuroscience

Variational Autoencoder for Dimensionality Reduction of Time-Series

Metagem ⭐ 155

💎 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, produce causal graphs and dynamical models.

Tangram ⭐ 153

Spatial alignment of single cell transcriptomic data.

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Pterasoftware ⭐ 136

Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.

Python3 binding to mRMR Feature Selection algorithm (currently not maintained)

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Compbiodatasetsformachinelearning ⭐ 120

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

Fitness landscape exploration sandbox for biological sequence design.

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

Dna2vec ⭐ 103

dna2vec: Consistent vector representations of variable-length k-mers

Python_biologist ⭐ 101

Python Programming for Biologists

Race and ethnicity Imputation from Disease history with Deep LEarning

🧬 An R package for visualizing molecular data in 3D

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Computational Cryoem ⭐ 73

A curated list of awesome computational cryo-EM methods.

Diffdock Pp ⭐ 73

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Cassiopeia ⭐ 67

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

Source code for "Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures"

An R Package for Geneset Enrichment Workflows

Biosimspace ⭐ 64

Code and resources for the EPSRC BioSimSpace project.

The Biochemical Algorithms Library

Guideline For Computational Biology And Bioinformatics ⭐ 60

The MPI Bioinformatics Toolkit

Pyscreener ⭐ 56

pythonic interface to virtual screening software

a modeling environment tailored to parameter estimation in dynamical systems

Shinyheatmap ⭐ 54

Web application for enormous biological heatmaps

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction

Biosimspace ⭐ 48

An interoperable Python framework for biomolecular simulation.

C.origami ⭐ 47

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

Glycowork ⭐ 46

Package for processing and analyzing glycans and their role in biology.

FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

A library to build and execute typed scientific workflows

Msk Staple ⭐ 43

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

Awesome Computational Biology ⭐ 43

Awesome list of computational biology.

A D library for computational biology and bioinformatics

Список вакансий в Департаменте Вычислительной Биологии в компании BIOCAD

Natural language processing of Gene Expression Omnibus data

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

10x Genomics Reads Simulator

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Ten_great_papers ⭐ 35

Ten great papers for wet lab biologists starting out in computational biology

Physics Aware Multiplex Gnn ⭐ 35

Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"

Python implementation of Spatial Analysis of Functional Enrichment (SAFE)

Pycontact ⭐ 34

Analysis of non-covalent interactions in MD trajectories

Myokit: A simple interface to cardiac cellular electrophysiology

Interpretable genotype-phenotype landscape modeling

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

Python API for the Interactive Tree of Life (iTOL)

Contact_map ⭐ 31

Contact map analysis for biomolecules; based on MDTraj

Artistoo ⭐ 30

CPM implementation in pure JavaScript

Compbioftw ⭐ 30

Essential introductory materials to get into computational biology.

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

Im2im Uq ⭐ 29

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations (EMNLP 2023)

Biosymbols.jl ⭐ 28

Nucleic and amino acid primitive types

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Python libraries and utilities for computational biology

Workflows ⭐ 28

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Soapdenovo Trans ⭐ 27

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

Causalpath ⭐ 27

A project for exploring differentially active signaling paths related to proteomics datasets

Straindesign ⭐ 27

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

☄️ Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments

pyQms, generalized, fast and accurate mass spectrometry data quantification

1-100 of 249 search results

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