anndata is a Python library for storing and manipulating annotated data matrices (especially single‑cell omics) in memory and on disk, with sparse data support, lazy operations, Dask/Zarr backends and a PyTorch interface.
Bio3D is an R package for structural bioinformatics that reads and processes PDB and trajectory data to perform alignment, PCA, normal mode analysis, network and ensemble analyses, enabling comparative and dynamic studies of proteins.
Bioconductor is an open-source ecosystem of R packages, tools, and containers for rigorous, reproducible analysis of high-throughput biological data—providing statistical methods, annotations, and infrastructure for genomics and related workflows.
Biopython — an open-source Python library for computational molecular biology that supplies parsers, data structures and utilities for sequence analysis, alignments, phylogenetics, structural biology and BioSQL/BLAST integration.
Biotite is a Python library for computational molecular biology that offers NumPy-like data structures and fast, modular tools for sequence and 3D structure analysis, file I/O, database access, visualization, and external-tool integration.
COBRApy is an open-source Python library for constraint-based reconstruction and analysis of metabolic networks, providing model construction, FBA/FVA, gene/reaction deletion, dFBA, sampling and solver-agnostic optimization for genome‑scale studies.
DeepChem is an open-source Python library that democratizes machine learning for chemistry, biology, materials and quantum applications by providing datasets, featurizers, models, and deployment tools to accelerate scientific ML workflows.
DNA Chisel is a Python 3 library and CLI/web tool for automated DNA sequence optimization under hard constraints and tunable objectives — e.g., codon optimization, restriction-site removal, GC tuning, homology avoidance and primer-friendly design.
HTSeq is an open-source Python library and command-line toolkit for processing high-throughput sequencing data, offering robust read counting (including cell barcodes and UMIs), feature-level quantification, and programmatic access for custom analyses.
libSBML is an open-source C/C++ library with multi-language bindings for reading, writing, validating, converting and programmatically manipulating SBML models, including full SBML Level 3 package support and unit/dimensional checks.
MDAnalysis is a Python library for loading, querying and analysing molecular dynamics trajectories and structures; it offers memory-efficient frame-by-frame access, a powerful selection language, many built‑in analyses, and an extensible API.
Nextflow is a dataflow DSL and workflow engine for building scalable, portable, and reproducible computational pipelines that run locally, on HPC schedulers, cloud providers or Kubernetes with container and Git integration.
