khmer

Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.

Unified Python framework for bulk, single-cell, and spatial RNA-seq multi-omics analysis with deep learning deconvolution (VAE) and graph neural networks, bridging Bindea, Bindea, scanpy and squidpy ecosystems (Nature Communications 2024)

Unified framework for state-of-the-art pre-trained bio foundation models across genomics and transcriptomics, providing standardized interfaces and pipelines for DNA, RNA, and single-cell models including Evo 2, Geneformer, scGPT, and UCE with streamlined inference, benchmarking, and fine-tuning workflows (213+ stars, 2024-2025)

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.

Sequence manipulation toolkit for FASTA/FASTQ files written in Nim.

BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.