Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
Repository Index
47,133 repositories indexed
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An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
VexCL is a C++ vector expression template library for OpenCL/CUDA/OpenMP
- opencl
- cuda
- c-plus-plus
- gpgpu
A flexible framework for solving PDEs with modern spectral methods.
- spectral-methods
- fluid-dynamics
- pde-solver
: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
⚗ A package useful for chemistry written in Python
- chemistry
- physical-chemistry
- chemical-kinetics
- chemical-formulas
A Free and Open Source Python Library for Multiobjective Optimization
- optimization
- multiobjective
- evolutionary
- algorithm
Numerical linear algebra software package
- linear-algebra
- hpc
- gpu-computing
- cuda
Module for statistical learning, with a particular emphasis on time-dependent modelling
- machine-learning
- python
- point-process
- optimization
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
2D/3D simplicial mesh generator interface for Python (Triangle, TetGen, gmsh)
- python
- mesh-generation
- scientific-computing
- triangle
The open source air traffic simulator
- python
- traffic
- aircraft
- simulation
A unit handling library for ruby
- ruby
- unit-math
- conversions
- temperature-units
A Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.
- optimization
- optimization-algorithms
- optimization-methods
- optimization-problem
Dicoogle - Open Source PACS
- dicoogle
- dicom
- pacs
- medical-imaging
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
- histopathology-images
- microscopy
- sliding-windows
- medical-image-analysis
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
C library for reading virtual slide images
- pathology
- whole-slide-imaging
- c
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
A Python native dynamical system simulation framework in the block diagram paradigm.
- blockdiagram
- control-systems
- hierarchical-modeling
- nonlinear-dynamics
a numpy-like fast vector module for micropython, circuitpython, and their derivatives
- micropython-ulab
- numpy
- micropython
- module
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.