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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34 of 6,223 resources
A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.
An ultrafast protein aligner for `blastp` and `blastx` like searches.
SPAdes (St. Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines and the de-facto standard for prokaryotic genome assemblies.
High-performance molecular simulation toolkit
LLMs as copilots for theorem proving in Lean 4, exposing native tactics (`suggest_tactics`, `search_proof`, `select_premises`) that embed language model inference and premise retrieval directly inside the Lean proof environment, supporting local CTranslate2/CUDA inference as well as remote model APIs for interactive and automated proof search (Caltech & NVIDIA, NeurIPS 2024, 1.2K+ stars)
An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
A haplotype-resolved assembler for accurate Hifi reads.
A Flexible Model For Record Linkage
The modern C++ library for sequence analysis.
Structural variant discovery by integrated paired-end and split-read analysis.
A small <720Kb C++ windows utility. That allows you to load Ancestry, 23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert them to Ancestry format. But also create files from peer reviewed publications to compare with you loaded data to give your genetic disposition for the condition you have entered the data for an statistical risk if OR values are included. Included with the program are example files for Type 2 Diabetes risk factors. (As I have type 2 Diabetes so I could test the results).
A software package for estimating gene and isoform expression levels from RNA-Seq data.
Bayesian haplotype-based polymorphism discovery and genotyping.
Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP).
Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.
A C++ library for parsing and manipulating VCF files.
maeparser is a parser for Schrodinger Maestro files.
Deep learning framework for molecular docking extending AutoDock Vina with convolutional neural network scoring functions, achieving superior virtual screening enrichment and pose prediction across diverse target classes; widely adopted in pharmaceutical structure-based drug design (J. Cheminformatics, 915+ stars, actively maintained)
A single molecule sequence assembler for genomes large and small.
A polymorphic bayesian genotyping model with wide applicability.
Structural variant and indel caller for mapped sequencing data.
Tandem repeat genotyping with long reads, being a modified version of HipSTR.
MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
Collection of tools for working with BAM files.
VCF manipulation and statistics (e.g. linkage disequilibrium, allele frequency, Fst).
A system for rapidly aligning entire genomes, whether in complete or draft form.
SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.
Scalable gVCF merging and joint variant calling for population sequencing projects
A generic C++ trie search tree library for small alphabets, allowing customizable leaf node structures and supporting approximate matching and word generation.
Standalone C library for assembling Illumina short reads in small regions
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Telseq is a tool for estimating telomere length from whole genome sequence data.