Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
- bioinformatics
- sequence-alignment
- genomics
- fm-index
Repository Index
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Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
Implementation of Alphafold 3 from Google Deepmind in Pytorch
- artificial-intelligence
- deep-learning
- attention-mechanisms
- denoising-diffusion
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
- artificial-intelligence
- deep-learning
- protein-folding
- attention-mechanism
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
- bioinformatics
- cross-platform
- fasta
- golang
Biological foundation modeling from molecular to genome scale
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.
- ai-agents
- bioinformatics
- equity
- genomics
An open-source application for biological image analysis
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Cloud-native genomic dataframes and batch computing
- genetics
- vcf
- genomics
- gwas
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
C library for high-throughput sequencing data formats
- htslib
- bioinformatics
- sam
- bam
Foundation Models for Genomics & Transcriptomics
:christmas_tree:Visualization and annotation of phylogenetic trees
- r
- visualization
- phylogenetic-trees
- annotations
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
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
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
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
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