Find open-source science resources
A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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6 of 5,923 resources
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.
A database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler
Utility that performs integrated analyses of 'gene' data (a set of genes or other genomic features) with 'peak' data (a set of regions, for example ChIP peaks) to identify the genes nearest to each peak, and vice versa.
NanoporeDB is an open-access structural database dedicated to the exploration, analysis, and design of protein nanopores, which serve as essential molecular gateways in biological membranes and form the basis of many advanced biosensing and sequencing technologies. This platform integrates large-scale structure-guided mining and deep learning-based modeling using AlphaFold-Multimer and AlphaFold3 to provide about 7,000 high-confidence multimeric nanopore structures. Each entry includes detailed information on membrane embedding, pore geometry annotation, and constriction profiling to support functional and biophysical interpretation. Through an interactive 3D visualization interface and quantitative parameters such as tilt angle, insertion depth, and pore geometry, NanoporeDB enables researchers to explore nanopore diversity, discover novel scaffolds, and accelerate innovation in molecular sensing, precision diagnostics, and synthetic biology.
A comprehensive R package for identifying and ranking influential nodes in biological and other complex networks. The package implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. It also provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures.