Foundation Models for Genomics & Transcriptomics
Repository Index
47,133 repositories indexed
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Scientific-grade astronomy routines for Python
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
Polygonal Surface Reconstruction from Point Clouds (C++ & Python)
- surface-reconstruction
- urban-modeling
- urban-reconstruction
- primitive-extraction
Open-source cross-platform symbolic algebra library for C# and F#. Can be used for both production and research purposes.
- csharp
- algebra
- integration
- latex
OpenMDAO repository.
- nasa
- open-source
- framework
- openmdao
3D medical imaging reconstruction software
- dicom
- dicom-viewer
- magnetic-resonance-imaging
- medical-image-processing
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Pathology Foundation Model - Nature Medicine
- foundation
- foundation-model
- histopathology
- mahmoodlab
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
- deep-learning
- pytorch
- deep-chemistry
- graph-neural-network
:triangular_ruler: Numerical integration (quadrature, cubature) in Python
- quadrature
- integration
- mathematics
- engineering
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.
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
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
Clinical Histopathology Imaging Evaluation Foundation Model
A flexible framework for solving PDEs with modern spectral methods.
- spectral-methods
- fluid-dynamics
- pde-solver
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
Official release of the ProGen models
- language-model
- protein
- generative-model
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)