ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Repository Index
47,133 repositories indexed
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WebGL accelerated JavaScript molecular graphics library
- molecular-graphics
- molecular-modeling
- computational-biology
- computational-chemistry
Geometry, simplified.
- swift
- geometry
- trigonometry
- coregraphics
This rocq library aims to formalize a substantial body of mathematics using the univalent point of view.
- coq
- mathematics
- unimath
- coq-library
A coupling library and ecosystem for partitioned multi-physics and multi-scale simulations, including surface and volume coupling.
- multi-physics
- fluid-structure-interaction
- high-performance-computing
- conjugate-heat-transfer
:spider_web: Gmsh for Python
- python
- pypi
- mesh-generation
- engineering
C library for high-throughput sequencing data formats
- htslib
- bioinformatics
- sam
- bam
Foundation Models for Genomics & Transcriptomics
:four_leaf_clover: Evolutionary optimization library for Go (genetic algorithm, partical swarm optimization, differential evolution)
Parallel solvers for sparse linear systems featuring multigrid methods.
- math-physics
- library
- hpc
- radiuss
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
:triangular_ruler: Numerical integration (quadrature, cubature) in Python
- quadrature
- integration
- mathematics
- engineering
Throw in the towel.
- dotnet
- towel
- csharp
- library
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
A flexible framework for solving PDEs with modern spectral methods.
- spectral-methods
- fluid-dynamics
- pde-solver
RBDL is a C++ library that contains some essential and efficient rigid body dynamics algorithms such as the Articulated Body Algorithm (ABA) for forward dynamics, Recursive Newton-Euler Algorithm (RNEA) for inverse dynamics, the Composite Rigid Body Algorithm (CRBA) for the efficient computation of the joint space inertia matrix and is also able to compute forward dynamics with external contact constraints and collision impulses. Furthermore it has some basic support for forward and inverse kinematics.
- articulated-body-algorithm
- inverse-dynamics
- forward-dynamics
- multi-body-dynamics
:1234: Bits, bytes and general-purpose calculator
- storage
- storage-unit-converter
- command-line
- standalone
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
Fast, sensitive and accurate integration of single-cell data with Harmony