Open source code for AlphaFold 2.
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AlphaFold 3 inference pipeline.
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
Code for the ProteinMPNN paper
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
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
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
Open Frontier Biomolecular Intelligence
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
talk with NCBI entrez using R
scPerturb: A resource and a python/R tool for single-cell perturbation data
- cite-seq
- database
- perturbation
- scatac-seq
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.