Biomni: a general-purpose biomedical AI agent
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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
- tensorflow
- deep-neural-network
- genomics
- science
Code for running RFdiffusion
Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
- openworm
- elegans
- biology
- simulation
Single-cell analysis in Python. Scales to >100M cells.
- machine-learning
- data-science
- visualize-data
- transcriptomics
NeuroKit2: The Python Toolbox for Neurophysiological Signal Processing
- python
- ecg
- eda
- emg
RNA-seq aligner
This package contains deep learning models and related scripts for RoseTTAFold
MMseqs2: ultra fast and sensitive search and clustering suite
- bioinformatics
- sequence-clustering
- profile-search
- sequence-search
Chai-1, SOTA model for biomolecular structure prediction
Tools (written in C using htslib) for manipulating next-generation sequencing data
Data intensive science for everyone.
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
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.
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
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models